├── 2016 ├── main.docx ├── main.log ├── main.pdf ├── main.synctex.gz ├── Khmer_Sangam_MN.ttf ├── Manhattan_maternal_LDL_8_17_16.png ├── Manhattan_paternal_LDL_8_17_16.png ├── README.md ├── main.aux ├── report2016.bib ├── main.doc └── main.tex ├── 2017 ├── main.docx ├── main.pdf ├── main.synctex.gz ├── README.md ├── main.blg ├── main.aux ├── main.bbl ├── report2017.bib ├── main.tex ├── main.log └── main.doc ├── 2018 ├── main.docx ├── main.pdf ├── main.synctex.gz ├── README.md ├── main.aux ├── main.blg ├── main.bbl ├── report2018.bib ├── main.doc ├── main.tex └── main.log ├── README.md └── LICENSE /2016/main.docx: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/smozaffari/CommitteeMeetingReports/HEAD/2016/main.docx -------------------------------------------------------------------------------- /2016/main.log: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/smozaffari/CommitteeMeetingReports/HEAD/2016/main.log -------------------------------------------------------------------------------- /2016/main.pdf: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/smozaffari/CommitteeMeetingReports/HEAD/2016/main.pdf -------------------------------------------------------------------------------- /2017/main.docx: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/smozaffari/CommitteeMeetingReports/HEAD/2017/main.docx -------------------------------------------------------------------------------- /2017/main.pdf: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/smozaffari/CommitteeMeetingReports/HEAD/2017/main.pdf -------------------------------------------------------------------------------- /2018/main.docx: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/smozaffari/CommitteeMeetingReports/HEAD/2018/main.docx -------------------------------------------------------------------------------- /2018/main.pdf: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/smozaffari/CommitteeMeetingReports/HEAD/2018/main.pdf -------------------------------------------------------------------------------- /2016/main.synctex.gz: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/smozaffari/CommitteeMeetingReports/HEAD/2016/main.synctex.gz -------------------------------------------------------------------------------- /2017/main.synctex.gz: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/smozaffari/CommitteeMeetingReports/HEAD/2017/main.synctex.gz -------------------------------------------------------------------------------- /2018/main.synctex.gz: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/smozaffari/CommitteeMeetingReports/HEAD/2018/main.synctex.gz -------------------------------------------------------------------------------- /2016/Khmer_Sangam_MN.ttf: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/smozaffari/CommitteeMeetingReports/HEAD/2016/Khmer_Sangam_MN.ttf -------------------------------------------------------------------------------- /README.md: -------------------------------------------------------------------------------- 1 | # CommitteeMeetingReports 2 | Committee Meeting Reports - LaTeX 3 | 4 | 5 | UChicago Genetics PhD Committee Meeting Reports. 6 | -------------------------------------------------------------------------------- /2016/Manhattan_maternal_LDL_8_17_16.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/smozaffari/CommitteeMeetingReports/HEAD/2016/Manhattan_maternal_LDL_8_17_16.png -------------------------------------------------------------------------------- /2016/Manhattan_paternal_LDL_8_17_16.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/smozaffari/CommitteeMeetingReports/HEAD/2016/Manhattan_paternal_LDL_8_17_16.png -------------------------------------------------------------------------------- /2016/README.md: -------------------------------------------------------------------------------- 1 | # 2016CommitteeMeeting 2 | 3 | ## Committee Meeting progress report 4 | 5 | 6 | 1. export .bib from Papers --> report2016.bib 7 | 8 | 2. open and edit in TeX 9 | 10 | 3. typset LaTeX 11 | 12 | 4. typset BibTeX 13 | 14 | 5. typeset LaTeX 15 | 16 | 17 | 18 | Optional: can use pandoc to convert to .doc to send to PI to edit : 19 | 20 | `pandoc main.tex -S --bibliography=report2016.bib -o main.docx` 21 | -------------------------------------------------------------------------------- /2017/README.md: -------------------------------------------------------------------------------- 1 | # 2017CommitteeMeeting 2 | 3 | ## Committee Meeting progress report 4 | 5 | 6 | 1. export .bib from Papers --> report2017.bib 7 | 8 | 2. open and edit in TeX 9 | 10 | 3. typset LaTeX 11 | 12 | 4. typset BibTeX 13 | 14 | 5. typeset LaTeX 15 | 16 | 17 | 18 | Optional: can use pandoc to convert to .doc to send to PI to edit : 19 | 20 | `pandoc main.tex -S --bibliography=report2017.bib -o main.docx` 21 | -------------------------------------------------------------------------------- /2018/README.md: -------------------------------------------------------------------------------- 1 | # 2018CommitteeMeeting 2 | 3 | ## Committee Meeting progress report 4 | 5 | 6 | 1. export .bib from Papers --> report2018.bib 7 | 8 | 2. open and edit in TeX 9 | 10 | 3. typset LaTeX 11 | 12 | 4. typset BibTeX 13 | 14 | 5. typeset LaTeX 15 | 16 | 17 | 18 | Optional: can use pandoc to convert to .doc to send to PI to edit : 19 | 20 | `pandoc main.tex -S --bibliography=report2018.bib -o main.docx` 21 | -------------------------------------------------------------------------------- /2018/main.aux: -------------------------------------------------------------------------------- 1 | \relax 2 | \citation{Mozaffari:loXwTR9q} 3 | \citation{Mozaffari:dg} 4 | \citation{Shiquan:G-C-HqrA} 5 | \citation{Hart:2018cv} 6 | \citation{Igartua:2017ir} 7 | \citation{Gamazon:2015fa} 8 | \citation{Mozaffari:dg} 9 | \bibdata{report2018} 10 | \bibcite{Gamazon:2015fa}{{1}{2015}{{Gamazon et~al.}}{{}}} 11 | \bibcite{Hart:2018cv}{{2}{2018}{{Hart et~al.}}{{}}} 12 | \bibcite{Igartua:2017ir}{{3}{2017}{{Igartua et~al.}}{{}}} 13 | \bibcite{Mozaffari:dg}{{4}{2017}{{Mozaffari et~al.}}{{}}} 14 | \bibcite{Mozaffari:loXwTR9q}{{5}{2018}{{Mozaffari et~al.}}{{}}} 15 | \bibcite{Shiquan:G-C-HqrA}{{6}{2018}{{Shiquan et~al.}}{{}}} 16 | \bibstyle{apalike} 17 | -------------------------------------------------------------------------------- /2018/main.blg: -------------------------------------------------------------------------------- 1 | This is BibTeX, Version 0.99d (TeX Live 2015) 2 | Capacity: max_strings=35307, hash_size=35307, hash_prime=30011 3 | The top-level auxiliary file: main.aux 4 | The style file: apalike.bst 5 | Database file #1: report2018.bib 6 | Warning--empty note in Mozaffari:loXwTR9q 7 | Warning--empty note in Shiquan:G-C-HqrA 8 | You've used 6 entries, 9 | 1935 wiz_defined-function locations, 10 | 509 strings with 5170 characters, 11 | and the built_in function-call counts, 2893 in all, are: 12 | = -- 255 13 | > -- 213 14 | < -- 0 15 | + -- 78 16 | - -- 78 17 | * -- 290 18 | := -- 541 19 | add.period$ -- 16 20 | call.type$ -- 6 21 | change.case$ -- 69 22 | chr.to.int$ -- 6 23 | cite$ -- 8 24 | duplicate$ -- 73 25 | empty$ -- 140 26 | format.name$ -- 84 27 | if$ -- 518 28 | int.to.chr$ -- 1 29 | int.to.str$ -- 0 30 | missing$ -- 4 31 | newline$ -- 31 32 | num.names$ -- 18 33 | pop$ -- 59 34 | preamble$ -- 1 35 | purify$ -- 69 36 | quote$ -- 0 37 | skip$ -- 57 38 | stack$ -- 0 39 | substring$ -- 146 40 | swap$ -- 4 41 | text.length$ -- 0 42 | text.prefix$ -- 0 43 | top$ -- 0 44 | type$ -- 36 45 | warning$ -- 2 46 | while$ -- 17 47 | width$ -- 0 48 | write$ -- 73 49 | (There were 2 warnings) 50 | -------------------------------------------------------------------------------- /2017/main.blg: -------------------------------------------------------------------------------- 1 | This is BibTeX, Version 0.99d (TeX Live 2017) 2 | Capacity: max_strings=100000, hash_size=100000, hash_prime=85009 3 | The top-level auxiliary file: main.aux 4 | The style file: apalike.bst 5 | Database file #1: report2017.bib 6 | Warning--I didn't find a database entry for "Hart:2017vg" 7 | Warning--I didn't find a database entry for "Igartua:2017fg" 8 | You've used 8 entries, 9 | 1935 wiz_defined-function locations, 10 | 538 strings with 6414 characters, 11 | and the built_in function-call counts, 5110 in all, are: 12 | = -- 446 13 | > -- 424 14 | < -- 0 15 | + -- 160 16 | - -- 160 17 | * -- 540 18 | := -- 927 19 | add.period$ -- 24 20 | call.type$ -- 8 21 | change.case$ -- 120 22 | chr.to.int$ -- 8 23 | cite$ -- 8 24 | duplicate$ -- 111 25 | empty$ -- 233 26 | format.name$ -- 168 27 | if$ -- 921 28 | int.to.chr$ -- 1 29 | int.to.str$ -- 0 30 | missing$ -- 8 31 | newline$ -- 43 32 | num.names$ -- 24 33 | pop$ -- 106 34 | preamble$ -- 1 35 | purify$ -- 120 36 | quote$ -- 0 37 | skip$ -- 81 38 | stack$ -- 0 39 | substring$ -- 277 40 | swap$ -- 8 41 | text.length$ -- 0 42 | text.prefix$ -- 0 43 | top$ -- 0 44 | type$ -- 48 45 | warning$ -- 0 46 | while$ -- 30 47 | width$ -- 0 48 | write$ -- 105 49 | (There were 2 warnings) 50 | -------------------------------------------------------------------------------- /2017/main.aux: -------------------------------------------------------------------------------- 1 | \relax 2 | \citation{Hart:2017vg} 3 | \citation{Mozaffari:dg} 4 | \citation{Igartua:2017fg} 5 | \citation{Gamazon:2015fa} 6 | \citation{Mozaffari:dg} 7 | \citation{Mott2014} 8 | \citation{Dobin:2012fg} 9 | \citation{Jun:2012je} 10 | \citation{vandeGeijn:2015hi} 11 | \citation{Docherty:2014cx} 12 | \citation{Baran:2015cx} 13 | \citation{Baran:2015cx} 14 | \citation{Baran:2015cx} 15 | \bibdata{report2017} 16 | \bibcite{Baran:2015cx}{{1}{2015}{{Baran et~al.}}{{}}} 17 | \newlabel{Zscore}{{1}{3}} 18 | \newlabel{signtest}{{2}{3}} 19 | \newlabel{my_first_eqn}{{3}{3}} 20 | \newlabel{poeqtl}{{4}{3}} 21 | \newlabel{poeqtl_maternal}{{5}{3}} 22 | \bibcite{Dobin:2012fg}{{2}{2012}{{Dobin et~al.}}{{}}} 23 | \bibcite{Docherty:2014cx}{{3}{2014}{{Docherty et~al.}}{{}}} 24 | \bibcite{Gamazon:2015fa}{{4}{2015}{{Gamazon et~al.}}{{}}} 25 | \bibcite{Jun:2012je}{{5}{2012}{{Jun et~al.}}{{}}} 26 | \bibcite{Mott2014}{{6}{2014}{{Mott et~al.}}{{}}} 27 | \bibcite{Mozaffari:dg}{{7}{2017}{{Mozaffari et~al.}}{{}}} 28 | \bibcite{vandeGeijn:2015hi}{{8}{2015}{{van~de Geijn et~al.}}{{}}} 29 | \bibstyle{apalike} 30 | \@writefile{lot}{\contentsline {table}{\numberline {1}{\ignorespaces Significant genes from sign test (p-values in column 3) with weighted Z score with corresponding p-values in column 4 and 5, respectively. Imprinted as defined by geneimprint.com database. }}{4}} 31 | \newlabel{tab:Significant Genes}{{1}{4}} 32 | -------------------------------------------------------------------------------- /2016/main.aux: -------------------------------------------------------------------------------- 1 | \relax 2 | \citation{Gamazon} 3 | \citation{Cusanovich} 4 | \@writefile{lof}{\contentsline {figure}{\numberline {1}{\ignorespaces Paternal and Maternal allele PO- GWAS Manhattan plots for LDL.}}{3}} 5 | \newlabel{fig:POGWAS}{{1}{3}} 6 | \@writefile{lot}{\contentsline {table}{\numberline {1}{\ignorespaces Phenotypes with Significant Maternal or Paternal Allele Associations.}}{3}} 7 | \newlabel{tab:Signif}{{1}{3}} 8 | \citation{Dobin} 9 | \citation{Jun} 10 | \citation{van de Geijn} 11 | \bibcite{Gamazon}{1} 12 | \newlabel{my_first_eqn}{{1}{4}} 13 | \@writefile{lot}{\contentsline {table}{\numberline {2}{\ignorespaces Paternally Imprinted (maternally expressed) genes significant from the Asymmetry test (p-values in column 3); top 17 genes with p-value 0. Known imprinting status in column 2, and Shapiro test p-value in column 4. Colored in pink are known paternally imprinted genes from geneimprint.com.}}{4}} 14 | \newlabel{tab:PaternalGenes}{{2}{4}} 15 | \@writefile{lot}{\contentsline {table}{\numberline {3}{\ignorespaces Maternally Imprinted (paternally expressed) genes significant from the Asymmetry test (p-values in column 3); top 17 genes with p-value 0. Known imprinting status in column 2, and Shapiro test p-value in column 4. Colored in blue are known maternally imprinted genes from geneimprint.com.}}{4}} 16 | \newlabel{tab:MaternalGenes}{{3}{4}} 17 | \bibcite{Cusanovich}{2} 18 | \bibcite{Dobin}{3} 19 | \bibcite{Jun}{4} 20 | \bibcite{van de Geijn}{5} 21 | -------------------------------------------------------------------------------- /2018/main.bbl: -------------------------------------------------------------------------------- 1 | \begin{thebibliography}{} 2 | 3 | \bibitem[Gamazon et~al., 2015]{Gamazon:2015fa} 4 | Gamazon, E.~R., Wheeler, H.~E., Shah, K.~P., Mozaffari, S.~V., Aquino-Michaels, 5 | K., Carroll, R.~J., Eyler, A.~E., Denny, J.~C., Nicolae, D.~L., Cox, N.~J., 6 | and Im, H.~K. (2015). 7 | \newblock {A gene-based association method for mapping traits using reference 8 | transcriptome data}. 9 | \newblock {\em Nature Genetics}, 47(9):1091--1098. 10 | 11 | \bibitem[Hart et~al., 2018]{Hart:2018cv} 12 | Hart, M.~W., Stover, D.~A., Guerra, V., Mozaffari, S.~V., Ober, C., Mugal, 13 | C.~F., and Kaj, I. (2018). 14 | \newblock {Positive selection on human gamete-recognition genes}. 15 | \newblock {\em PeerJ}, 6(1):e4259--35. 16 | 17 | \bibitem[Igartua et~al., 2017]{Igartua:2017ir} 18 | Igartua, C., Mozaffari, S.~V., Nicolae, D.~L., and Ober, C. (2017). 19 | \newblock {Rare non-coding variants are associated with plasma lipid traits in 20 | a founder population.} 21 | \newblock {\em Scientific Reports}, 7(1):16415. 22 | 23 | \bibitem[Mozaffari et~al., 2017]{Mozaffari:dg} 24 | Mozaffari, S.~V., DeCara, J.~M., Shah, S.~J., Lang, R.~M., Nicolae, D.~L., and 25 | Ober, C. (2017). 26 | \newblock {Parent of Origin Effects on Quantitative Phenotypes in a Founder 27 | Population}. 28 | \newblock {\em bioRxiv}. 29 | 30 | \bibitem[Mozaffari et~al., 2018]{Mozaffari:loXwTR9q} 31 | Mozaffari, S.~V., Stein, M.~M., Magnaye, K.~M., Nicolae, D.~L., and Ober, C. 32 | (2018). 33 | \newblock {Gene Expression and Methylation of Imprinted Genes in the 34 | Hutterites}. 35 | 36 | \bibitem[Shiquan et~al., 2018]{Shiquan:G-C-HqrA} 37 | Shiquan, S., Zhu, J., Mozaffari, S.~V., Ober, C., Chen, M., and Zhou, X. 38 | (2018). 39 | \newblock {Heritability Estimation and Differential Analysis with Generalized 40 | Linear Mixed Models in RNA Sequencing and Bisulfite Sequencing Studies}. 41 | 42 | \end{thebibliography} 43 | -------------------------------------------------------------------------------- /2017/main.bbl: -------------------------------------------------------------------------------- 1 | \begin{thebibliography}{} 2 | 3 | \bibitem[Baran et~al., 2015]{Baran:2015cx} 4 | Baran, Y., Subramaniam, M., Biton, A., Tukiainen, T., Tsang, E.~K., Rivas, 5 | M.~A., Pirinen, M., Gutierrez-Arcelus, M., Smith, K.~S., Kukurba, K.~R., 6 | Zhang, R., Eng, C., Torgerson, D.~G., Urbanek, C., {GTEx Consortium}, Li, 7 | J.~B., Rodriguez-Santana, J.~R., Burchard, E.~G., Seibold, M.~A., MacArthur, 8 | D.~G., Montgomery, S.~B., Zaitlen, N.~A., and Lappalainen, T. (2015). 9 | \newblock {The landscape of genomic imprinting across diverse adult human 10 | tissues.} 11 | \newblock {\em Genome Research}, 25(7):927--936. 12 | 13 | \bibitem[Dobin et~al., 2012]{Dobin:2012fg} 14 | Dobin, A., Davis, C.~A., Schlesinger, F., Drenkow, J., Zaleski, C., Jha, S., 15 | Batut, P., Chaisson, M., and Gingeras, T.~R. (2012). 16 | \newblock {STAR: ultrafast universal RNA-seq aligner}. 17 | \newblock {\em Bioinformatics}, 29(1):15--21. 18 | 19 | \bibitem[Docherty et~al., 2014]{Docherty:2014cx} 20 | Docherty, L.~E., Rezwan, F.~I., Poole, R.~L., Jagoe, H., Lake, H., Lockett, 21 | G.~A., Arshad, H., Wilson, D.~I., Holloway, J.~W., Temple, I.~K., and Mackay, 22 | D. J.~G. (2014). 23 | \newblock {Genome-wide DNA methylation analysis of patients with imprinting 24 | disorders identifies differentially methylated regions associated with novel 25 | candidate imprinted genes.} 26 | \newblock {\em Journal of medical genetics}, 51(4):229--238. 27 | 28 | \bibitem[Gamazon et~al., 2015]{Gamazon:2015fa} 29 | Gamazon, E.~R., Wheeler, H.~E., Shah, K.~P., Mozaffari, S.~V., Aquino-Michaels, 30 | K., Carroll, R.~J., Eyler, A.~E., Denny, J.~C., Nicolae, D.~L., Cox, N.~J., 31 | and Im, H.~K. (2015). 32 | \newblock {A gene-based association method for mapping traits using reference 33 | transcriptome data}. 34 | \newblock {\em Nature Genetics}, 47(9):1091--1098. 35 | 36 | \bibitem[Jun et~al., 2012]{Jun:2012je} 37 | Jun, G., Flickinger, M., Hetrick, K.~N., Romm, J.~M., Doheny, K.~F., Abecasis, 38 | G.~R., Boehnke, M., and Kang, H.~M. (2012). 39 | \newblock {Detecting and Estimating Contamination of Human DNA Samples in 40 | Sequencing and Array-Based Genotype Data}. 41 | \newblock {\em The American Journal of Human Genetics}, 91(5):839--848. 42 | 43 | \bibitem[Mott et~al., 2014]{Mott2014} 44 | Mott, R., Yuan, W., Kaisaki, P., Gan, X., Cleak, J., Edwards, A., Baud, A., and 45 | Flint, J. (2014). 46 | \newblock {The Architecture of Parent-of-Origin Effects in Mice}. 47 | \newblock {\em Cell}, 156(1-2):332--342. 48 | 49 | \bibitem[Mozaffari et~al., 2017]{Mozaffari:dg} 50 | Mozaffari, S.~V., DeCara, J.~M., Shah, S.~J., Lang, R.~M., Nicolae, D.~L., and 51 | Ober, C. (2017). 52 | \newblock {Parent of Origin Effects on Quantitative Phenotypes in a Founder 53 | Population}. 54 | \newblock {\em bioRxiv}. 55 | 56 | \bibitem[van~de Geijn et~al., 2015]{vandeGeijn:2015hi} 57 | van~de Geijn, B., McVicker, G., Gilad, Y., and Pritchard, J.~K. (2015). 58 | \newblock {WASP: allele-specific software for robust molecular quantitative 59 | trait locus discovery}. 60 | \newblock {\em Nature Methods}, 12(11):1061--1063. 61 | 62 | \end{thebibliography} 63 | -------------------------------------------------------------------------------- /2016/report2016.bib: -------------------------------------------------------------------------------- 1 | %% Created using Papers on Mon, 11 Jun 2018. 2 | %% http://papersapp.com/papers/ 3 | 4 | @unpublished{Mozaffari:loXwTR9q, 5 | author = {Mozaffari, Sahar V and Stein, Michelle M and Magnaye, Kevin M and Nicolae, Dan L and Ober, Carole}, 6 | title = {{Gene Expression and Methylation of Imprinted Genes in the Hutterites}}, 7 | month = feb, 8 | year = {2018} 9 | } 10 | 11 | @unpublished{Shiquan:G-C-HqrA, 12 | author = {Shiquan, Sun and Zhu, Jiaqiang and Mozaffari, Sahar V and Ober, Carole and Chen, Mengjie and Zhou, Xiang}, 13 | title = {{Heritability Estimation and Differential Analysis with Generalized Linear Mixed Models in RNA Sequencing and Bisulfite Sequencing Studies}}, 14 | month = feb, 15 | year = {2018} 16 | } 17 | 18 | @article{Hart:2018cv, 19 | author = {Hart, Michael W and Stover, Daryn A and Guerra, Vanessa and Mozaffari, Sahar V and Ober, Carole and Mugal, Carina F and Kaj, Ingemar}, 20 | title = {{Positive selection on human gamete-recognition genes}}, 21 | journal = {PeerJ}, 22 | year = {2018}, 23 | volume = {6}, 24 | number = {1}, 25 | pages = {e4259--35} 26 | } 27 | 28 | @article{Igartua:2017uc, 29 | author = {Igartua, Catherine and Mozaffari, Sahar V and Nicolae, Dan L and Ober, Carole}, 30 | title = {{Rare non-coding variants are associated with plasma lipid traits in a founder population}}, 31 | year = {2017}, 32 | volume = {7}, 33 | number = {1}, 34 | pages = {16415} 35 | } 36 | 37 | @article{Mozaffari:dg, 38 | author = {Mozaffari, S V and DeCara, J M and Shah, S J and Lang, R M and Nicolae, Dan L and Ober, Carole}, 39 | title = {{Parent of Origin Effects on Quantitative Phenotypes in a Founder Population}}, 40 | journal = {bioRxiv}, 41 | year = {2017} 42 | } 43 | 44 | @article{Cusanovich:2016id, 45 | author = {Cusanovich, Darren A and Caliskan, Minal and Billstrand, Christine and Michelini, Katelyn and Chavarria, Claudia and De Leon, Sherryl and Mitrano, Amy and Lewellyn, Noah and Elias, Jack A and Chupp, Geoffrey L and Lang, Roberto M and Shah, Sanjiv J and Decara, Jeanne M and Gilad, Yoav and Ober, Carole}, 46 | title = {{Integrated analyses of gene expression and genetic association studies in a founder population.}}, 47 | journal = {Human Molecular Genetics}, 48 | year = {2016}, 49 | volume = {25}, 50 | number = {10}, 51 | pages = {2104--2112}, 52 | month = may 53 | } 54 | 55 | @article{Dobin:2012fg, 56 | author = {Dobin, Alexander and Davis, Carrie A and Schlesinger, Felix and Drenkow, Jorg and Zaleski, Chris and Jha, Sonali and Batut, Philippe and Chaisson, Mark and Gingeras, Thomas R}, 57 | title = {{STAR: ultrafast universal RNA-seq aligner}}, 58 | journal = {Bioinformatics}, 59 | year = {2012}, 60 | volume = {29}, 61 | number = {1}, 62 | pages = {15--21}, 63 | month = oct 64 | } 65 | 66 | @article{Gamazon:2015fa, 67 | author = {Gamazon, Eric R and Wheeler, Heather E and Shah, Kaanan P and Mozaffari, Sahar V and Aquino-Michaels, Keston and Carroll, Robert J and Eyler, Anne E and Denny, Joshua C and Nicolae, Dan L and Cox, Nancy J and Im, Hae Kyung}, 68 | title = {{A gene-based association method for mapping traits using reference transcriptome data}}, 69 | journal = {Nature Genetics}, 70 | year = {2015}, 71 | volume = {47}, 72 | number = {9}, 73 | pages = {1091--1098}, 74 | month = aug 75 | } 76 | 77 | @article{vandeGeijn:2015hi, 78 | author = {van de Geijn, Bryce and McVicker, Graham and Gilad, Yoav and Pritchard, Jonathan K}, 79 | title = {{WASP: allele-specific software for robust molecular quantitative trait locus discovery}}, 80 | journal = {Nature Methods}, 81 | year = {2015}, 82 | volume = {12}, 83 | number = {11}, 84 | pages = {1061--1063}, 85 | month = nov 86 | } 87 | 88 | @article{Mott2014, 89 | author = {Mott, Richard and Yuan, Wei and Kaisaki, Pamela and Gan, Xiangchao and Cleak, James and Edwards, Andrew and Baud, Amelie and Flint, Jonathan}, 90 | title = {{The Architecture of Parent-of-Origin Effects in Mice}}, 91 | journal = {Cell}, 92 | year = {2014}, 93 | volume = {156}, 94 | number = {1-2}, 95 | pages = {332--342}, 96 | month = jan 97 | } 98 | 99 | @article{Jun:2012je, 100 | author = {Jun, Goo and Flickinger, Matthew and Hetrick, Kurt N and Romm, Jane M and Doheny, Kimberly F and Abecasis, Goncalo R and Boehnke, Michael and Kang, Hyun Min}, 101 | title = {{Detecting and Estimating Contamination of Human DNA Samples in Sequencing and Array-Based Genotype Data}}, 102 | journal = {The American Journal of Human Genetics}, 103 | year = {2012}, 104 | volume = {91}, 105 | number = {5}, 106 | pages = {839--848}, 107 | month = nov 108 | } 109 | 110 | @article{Daelemans:2010kc, 111 | author = {Daelemans, Caroline and Ritchie, Matthew E and Smits, Guillaume and Abu-Amero, Sayeda and Sudbery, Ian M and Forrest, Matthew S and Campino, Susana and Clark, Taane G and Stanier, Philip and Kwiatkowski, Dominic and Deloukas, Panos and Dermitzakis, Emmanouil T and Tavar{\'e}, Simon and Moore, Gudrun E and Dunham, Ian}, 112 | title = {{High-throughput analysis of candidate imprinted genes and allele-specific gene expression in the human term placenta.}}, 113 | journal = {BMC genetics}, 114 | year = {2010}, 115 | volume = {11}, 116 | number = {1}, 117 | pages = {25}, 118 | month = apr 119 | } 120 | 121 | @article{Baran:2015cx, 122 | author = {Baran, Yael and Subramaniam, Meena and Biton, Anne and Tukiainen, Taru and Tsang, Emily K and Rivas, Manuel A and Pirinen, Matti and Gutierrez-Arcelus, Maria and Smith, Kevin S and Kukurba, Kim R and Zhang, Rui and Eng, Celeste and Torgerson, Dara G and Urbanek, Cydney and {GTEx Consortium} and Li, Jin Billy and Rodriguez-Santana, Jose R and Burchard, Esteban G and Seibold, Max A and MacArthur, Daniel G and Montgomery, Stephen B and Zaitlen, Noah A and Lappalainen, Tuuli}, 123 | title = {{The landscape of genomic imprinting across diverse adult human tissues.}}, 124 | journal = {Genome Research}, 125 | year = {2015}, 126 | volume = {25}, 127 | number = {7}, 128 | pages = {927--936}, 129 | month = jul 130 | } 131 | 132 | @article{Docherty:2014cx, 133 | author = {Docherty, Louise E and Rezwan, Faisal I and Poole, Rebecca L and Jagoe, Hannah and Lake, Hannah and Lockett, Gabrielle A and Arshad, Hasan and Wilson, David I and Holloway, John W and Temple, I Karen and Mackay, Deborah J G}, 134 | title = {{Genome-wide DNA methylation analysis of patients with imprinting disorders identifies differentially methylated regions associated with novel candidate imprinted genes.}}, 135 | journal = {Journal of medical genetics}, 136 | year = {2014}, 137 | volume = {51}, 138 | number = {4}, 139 | pages = {229--238}, 140 | month = apr 141 | } 142 | 143 | -------------------------------------------------------------------------------- /2017/report2017.bib: -------------------------------------------------------------------------------- 1 | %% Created using Papers on Mon, 11 Jun 2018. 2 | %% http://papersapp.com/papers/ 3 | 4 | @unpublished{Mozaffari:loXwTR9q, 5 | author = {Mozaffari, Sahar V and Stein, Michelle M and Magnaye, Kevin M and Nicolae, Dan L and Ober, Carole}, 6 | title = {{Gene Expression and Methylation of Imprinted Genes in the Hutterites}}, 7 | month = feb, 8 | year = {2018} 9 | } 10 | 11 | @unpublished{Shiquan:G-C-HqrA, 12 | author = {Shiquan, Sun and Zhu, Jiaqiang and Mozaffari, Sahar V and Ober, Carole and Chen, Mengjie and Zhou, Xiang}, 13 | title = {{Heritability Estimation and Differential Analysis with Generalized Linear Mixed Models in RNA Sequencing and Bisulfite Sequencing Studies}}, 14 | month = feb, 15 | year = {2018} 16 | } 17 | 18 | @article{Hart:2018cv, 19 | author = {Hart, Michael W and Stover, Daryn A and Guerra, Vanessa and Mozaffari, Sahar V and Ober, Carole and Mugal, Carina F and Kaj, Ingemar}, 20 | title = {{Positive selection on human gamete-recognition genes}}, 21 | journal = {PeerJ}, 22 | year = {2018}, 23 | volume = {6}, 24 | number = {1}, 25 | pages = {e4259--35} 26 | } 27 | 28 | @article{Igartua:2017uc, 29 | author = {Igartua, Catherine and Mozaffari, Sahar V and Nicolae, Dan L and Ober, Carole}, 30 | title = {{Rare non-coding variants are associated with plasma lipid traits in a founder population}}, 31 | year = {2017}, 32 | volume = {7}, 33 | number = {1}, 34 | pages = {16415} 35 | } 36 | 37 | @article{Mozaffari:dg, 38 | author = {Mozaffari, S V and DeCara, J M and Shah, S J and Lang, R M and Nicolae, Dan L and Ober, Carole}, 39 | title = {{Parent of Origin Effects on Quantitative Phenotypes in a Founder Population}}, 40 | journal = {bioRxiv}, 41 | year = {2017} 42 | } 43 | 44 | @article{Cusanovich:2016id, 45 | author = {Cusanovich, Darren A and Caliskan, Minal and Billstrand, Christine and Michelini, Katelyn and Chavarria, Claudia and De Leon, Sherryl and Mitrano, Amy and Lewellyn, Noah and Elias, Jack A and Chupp, Geoffrey L and Lang, Roberto M and Shah, Sanjiv J and Decara, Jeanne M and Gilad, Yoav and Ober, Carole}, 46 | title = {{Integrated analyses of gene expression and genetic association studies in a founder population.}}, 47 | journal = {Human Molecular Genetics}, 48 | year = {2016}, 49 | volume = {25}, 50 | number = {10}, 51 | pages = {2104--2112}, 52 | month = may 53 | } 54 | 55 | @article{Dobin:2012fg, 56 | author = {Dobin, Alexander and Davis, Carrie A and Schlesinger, Felix and Drenkow, Jorg and Zaleski, Chris and Jha, Sonali and Batut, Philippe and Chaisson, Mark and Gingeras, Thomas R}, 57 | title = {{STAR: ultrafast universal RNA-seq aligner}}, 58 | journal = {Bioinformatics}, 59 | year = {2012}, 60 | volume = {29}, 61 | number = {1}, 62 | pages = {15--21}, 63 | month = oct 64 | } 65 | 66 | @article{Gamazon:2015fa, 67 | author = {Gamazon, Eric R and Wheeler, Heather E and Shah, Kaanan P and Mozaffari, Sahar V and Aquino-Michaels, Keston and Carroll, Robert J and Eyler, Anne E and Denny, Joshua C and Nicolae, Dan L and Cox, Nancy J and Im, Hae Kyung}, 68 | title = {{A gene-based association method for mapping traits using reference transcriptome data}}, 69 | journal = {Nature Genetics}, 70 | year = {2015}, 71 | volume = {47}, 72 | number = {9}, 73 | pages = {1091--1098}, 74 | month = aug 75 | } 76 | 77 | @article{vandeGeijn:2015hi, 78 | author = {van de Geijn, Bryce and McVicker, Graham and Gilad, Yoav and Pritchard, Jonathan K}, 79 | title = {{WASP: allele-specific software for robust molecular quantitative trait locus discovery}}, 80 | journal = {Nature Methods}, 81 | year = {2015}, 82 | volume = {12}, 83 | number = {11}, 84 | pages = {1061--1063}, 85 | month = nov 86 | } 87 | 88 | @article{Mott2014, 89 | author = {Mott, Richard and Yuan, Wei and Kaisaki, Pamela and Gan, Xiangchao and Cleak, James and Edwards, Andrew and Baud, Amelie and Flint, Jonathan}, 90 | title = {{The Architecture of Parent-of-Origin Effects in Mice}}, 91 | journal = {Cell}, 92 | year = {2014}, 93 | volume = {156}, 94 | number = {1-2}, 95 | pages = {332--342}, 96 | month = jan 97 | } 98 | 99 | @article{Jun:2012je, 100 | author = {Jun, Goo and Flickinger, Matthew and Hetrick, Kurt N and Romm, Jane M and Doheny, Kimberly F and Abecasis, Goncalo R and Boehnke, Michael and Kang, Hyun Min}, 101 | title = {{Detecting and Estimating Contamination of Human DNA Samples in Sequencing and Array-Based Genotype Data}}, 102 | journal = {The American Journal of Human Genetics}, 103 | year = {2012}, 104 | volume = {91}, 105 | number = {5}, 106 | pages = {839--848}, 107 | month = nov 108 | } 109 | 110 | @article{Daelemans:2010kc, 111 | author = {Daelemans, Caroline and Ritchie, Matthew E and Smits, Guillaume and Abu-Amero, Sayeda and Sudbery, Ian M and Forrest, Matthew S and Campino, Susana and Clark, Taane G and Stanier, Philip and Kwiatkowski, Dominic and Deloukas, Panos and Dermitzakis, Emmanouil T and Tavar{\'e}, Simon and Moore, Gudrun E and Dunham, Ian}, 112 | title = {{High-throughput analysis of candidate imprinted genes and allele-specific gene expression in the human term placenta.}}, 113 | journal = {BMC genetics}, 114 | year = {2010}, 115 | volume = {11}, 116 | number = {1}, 117 | pages = {25}, 118 | month = apr 119 | } 120 | 121 | @article{Baran:2015cx, 122 | author = {Baran, Yael and Subramaniam, Meena and Biton, Anne and Tukiainen, Taru and Tsang, Emily K and Rivas, Manuel A and Pirinen, Matti and Gutierrez-Arcelus, Maria and Smith, Kevin S and Kukurba, Kim R and Zhang, Rui and Eng, Celeste and Torgerson, Dara G and Urbanek, Cydney and {GTEx Consortium} and Li, Jin Billy and Rodriguez-Santana, Jose R and Burchard, Esteban G and Seibold, Max A and MacArthur, Daniel G and Montgomery, Stephen B and Zaitlen, Noah A and Lappalainen, Tuuli}, 123 | title = {{The landscape of genomic imprinting across diverse adult human tissues.}}, 124 | journal = {Genome Research}, 125 | year = {2015}, 126 | volume = {25}, 127 | number = {7}, 128 | pages = {927--936}, 129 | month = jul 130 | } 131 | 132 | @article{Docherty:2014cx, 133 | author = {Docherty, Louise E and Rezwan, Faisal I and Poole, Rebecca L and Jagoe, Hannah and Lake, Hannah and Lockett, Gabrielle A and Arshad, Hasan and Wilson, David I and Holloway, John W and Temple, I Karen and Mackay, Deborah J G}, 134 | title = {{Genome-wide DNA methylation analysis of patients with imprinting disorders identifies differentially methylated regions associated with novel candidate imprinted genes.}}, 135 | journal = {Journal of medical genetics}, 136 | year = {2014}, 137 | volume = {51}, 138 | number = {4}, 139 | pages = {229--238}, 140 | month = apr 141 | } 142 | 143 | -------------------------------------------------------------------------------- /2018/report2018.bib: -------------------------------------------------------------------------------- 1 | %% Created using Papers on Mon, 26 Feb 2018. 2 | %% http://papersapp.com/papers/ 3 | 4 | @unpublished{Mozaffari:loXwTR9q, 5 | author = {Mozaffari, Sahar V and Stein, Michelle M and Magnaye, Kevin M and Nicolae, Dan L and Ober, Carole}, 6 | title = {{Gene Expression and Methylation of Imprinted Genes in the Hutterites}}, 7 | month = feb, 8 | year = {2018} 9 | } 10 | 11 | @unpublished{Shiquan:G-C-HqrA, 12 | author = {Shiquan, Sun and Zhu, Jiaqiang and Mozaffari, Sahar V and Ober, Carole and Chen, Mengjie and Zhou, Xiang}, 13 | title = {{Heritability Estimation and Differential Analysis with Generalized Linear Mixed Models in RNA Sequencing and Bisulfite Sequencing Studies}}, 14 | month = feb, 15 | year = {2018} 16 | } 17 | 18 | @article{Hart:2018cv, 19 | author = {Hart, Michael W and Stover, Daryn A and Guerra, Vanessa and Mozaffari, Sahar V and Ober, Carole and Mugal, Carina F and Kaj, Ingemar}, 20 | title = {{Positive selection on human gamete-recognition genes}}, 21 | journal = {PeerJ}, 22 | year = {2018}, 23 | volume = {6}, 24 | number = {1}, 25 | pages = {e4259--35} 26 | } 27 | 28 | @article{Mozaffari:dg, 29 | author = {Mozaffari, S V and DeCara, J M and Shah, S J and Lang, R M and Nicolae, Dan L and Ober, Carole}, 30 | title = {{Parent of Origin Effects on Quantitative Phenotypes in a Founder Population}}, 31 | journal = {bioRxiv}, 32 | year = {2017} 33 | } 34 | 35 | @article{Cusanovich:2016id, 36 | author = {Cusanovich, Darren A and Caliskan, Minal and Billstrand, Christine and Michelini, Katelyn and Chavarria, Claudia and De Leon, Sherryl and Mitrano, Amy and Lewellyn, Noah and Elias, Jack A and Chupp, Geoffrey L and Lang, Roberto M and Shah, Sanjiv J and Decara, Jeanne M and Gilad, Yoav and Ober, Carole}, 37 | title = {{Integrated analyses of gene expression and genetic association studies in a founder population.}}, 38 | journal = {Human Molecular Genetics}, 39 | year = {2016}, 40 | volume = {25}, 41 | number = {10}, 42 | pages = {2104--2112}, 43 | month = may 44 | } 45 | 46 | @article{Dobin:2012fg, 47 | author = {Dobin, Alexander and Davis, Carrie A and Schlesinger, Felix and Drenkow, Jorg and Zaleski, Chris and Jha, Sonali and Batut, Philippe and Chaisson, Mark and Gingeras, Thomas R}, 48 | title = {{STAR: ultrafast universal RNA-seq aligner}}, 49 | journal = {Bioinformatics}, 50 | year = {2012}, 51 | volume = {29}, 52 | number = {1}, 53 | pages = {15--21}, 54 | month = oct 55 | } 56 | 57 | @article{Gamazon:2015fa, 58 | author = {Gamazon, Eric R and Wheeler, Heather E and Shah, Kaanan P and Mozaffari, Sahar V and Aquino-Michaels, Keston and Carroll, Robert J and Eyler, Anne E and Denny, Joshua C and Nicolae, Dan L and Cox, Nancy J and Im, Hae Kyung}, 59 | title = {{A gene-based association method for mapping traits using reference transcriptome data}}, 60 | journal = {Nature Genetics}, 61 | year = {2015}, 62 | volume = {47}, 63 | number = {9}, 64 | pages = {1091--1098}, 65 | month = aug 66 | } 67 | 68 | @article{vandeGeijn:2015hi, 69 | author = {van de Geijn, Bryce and McVicker, Graham and Gilad, Yoav and Pritchard, Jonathan K}, 70 | title = {{WASP: allele-specific software for robust molecular quantitative trait locus discovery}}, 71 | journal = {Nature Methods}, 72 | year = {2015}, 73 | volume = {12}, 74 | number = {11}, 75 | pages = {1061--1063}, 76 | month = nov 77 | } 78 | 79 | @article{Igartua:2017fg, 80 | author = {Igartua, Catherine and Mozaffari, Sahar V and Nicolae, Dan and Ober, Carole}, 81 | title = {{Rare non-coding variants are associated with plasma lipid traits in a founder population}}, 82 | journal = {bioRxiv}, 83 | year = {2017}, 84 | month = may 85 | } 86 | 87 | @article{Jun:2012je, 88 | author = {Jun, Goo and Flickinger, Matthew and Hetrick, Kurt N and Romm, Jane M and Doheny, Kimberly F and Abecasis, Goncalo R and Boehnke, Michael and Kang, Hyun Min}, 89 | title = {{Detecting and Estimating Contamination of Human DNA Samples in Sequencing and Array-Based Genotype Data}}, 90 | journal = {The American Journal of Human Genetics}, 91 | year = {2012}, 92 | volume = {91}, 93 | number = {5}, 94 | pages = {839--848}, 95 | month = nov 96 | } 97 | 98 | @article{Mott2014, 99 | author = {Mott, Richard and Yuan, Wei and Kaisaki, Pamela and Gan, Xiangchao and Cleak, James and Edwards, Andrew and Baud, Amelie and Flint, Jonathan}, 100 | title = {{The Architecture of Parent-of-Origin Effects in Mice}}, 101 | journal = {Cell}, 102 | year = {2014}, 103 | volume = {156}, 104 | number = {1-2}, 105 | pages = {332--342}, 106 | month = jan 107 | } 108 | 109 | @article{Daelemans:2010kc, 110 | author = {Daelemans, Caroline and Ritchie, Matthew E and Smits, Guillaume and Abu-Amero, Sayeda and Sudbery, Ian M and Forrest, Matthew S and Campino, Susana and Clark, Taane G and Stanier, Philip and Kwiatkowski, Dominic and Deloukas, Panos and Dermitzakis, Emmanouil T and Tavar{\'e}, Simon and Moore, Gudrun E and Dunham, Ian}, 111 | title = {{High-throughput analysis of candidate imprinted genes and allele-specific gene expression in the human term placenta.}}, 112 | journal = {BMC genetics}, 113 | year = {2010}, 114 | volume = {11}, 115 | number = {1}, 116 | pages = {25}, 117 | month = apr 118 | } 119 | 120 | @article{Baran:2015cx, 121 | author = {Baran, Yael and Subramaniam, Meena and Biton, Anne and Tukiainen, Taru and Tsang, Emily K and Rivas, Manuel A and Pirinen, Matti and Gutierrez-Arcelus, Maria and Smith, Kevin S and Kukurba, Kim R and Zhang, Rui and Eng, Celeste and Torgerson, Dara G and Urbanek, Cydney and {GTEx Consortium} and Li, Jin Billy and Rodriguez-Santana, Jose R and Burchard, Esteban G and Seibold, Max A and MacArthur, Daniel G and Montgomery, Stephen B and Zaitlen, Noah A and Lappalainen, Tuuli}, 122 | title = {{The landscape of genomic imprinting across diverse adult human tissues.}}, 123 | journal = {Genome Research}, 124 | year = {2015}, 125 | volume = {25}, 126 | number = {7}, 127 | pages = {927--936}, 128 | month = jul 129 | } 130 | 131 | @article{Zhabotynsky:2017uj, 132 | author = {Zhabotynsky, V and Sun, W and Inoue, K and Magnuson, T}, 133 | title = {{Joint estimation of genetic and parent-of-origin effects using RNA-seq data from human}}, 134 | journal = {arXiv.org}, 135 | year = {2017}, 136 | eprint = {related:i6SipSPiTTIJ}, 137 | eprinttype = {scholar} 138 | } 139 | 140 | @article{Igartua:2017ir, 141 | author = {Igartua, Catherine and Mozaffari, Sahar V and Nicolae, Dan L and Ober, Carole}, 142 | title = {{Rare non-coding variants are associated with plasma lipid traits in a founder population.}}, 143 | journal = {Scientific Reports}, 144 | year = {2017}, 145 | volume = {7}, 146 | number = {1}, 147 | pages = {16415}, 148 | month = nov 149 | } 150 | 151 | @article{Docherty:2014cx, 152 | author = {Docherty, Louise E and Rezwan, Faisal I and Poole, Rebecca L and Jagoe, Hannah and Lake, Hannah and Lockett, Gabrielle A and Arshad, Hasan and Wilson, David I and Holloway, John W and Temple, I Karen and Mackay, Deborah J G}, 153 | title = {{Genome-wide DNA methylation analysis of patients with imprinting disorders identifies differentially methylated regions associated with novel candidate imprinted genes.}}, 154 | journal = {Journal of medical genetics}, 155 | year = {2014}, 156 | volume = {51}, 157 | number = {4}, 158 | pages = {229--238}, 159 | month = apr 160 | } 161 | 162 | -------------------------------------------------------------------------------- /2018/main.doc: -------------------------------------------------------------------------------- 1 |

Committee Meeting Report Sahar Mozaffari
2 | Professor: Carole Ober
3 | GGSB Matriculated 2013 Date: 3/8/18
4 |

5 |


6 | Progress since last Committee Meeting - October 2, 2017

7 |

Awards

8 | 14 |

Manuscripts in progress

15 | 20 |

Published

21 | 26 |

Oral Presentations

27 | 39 |

Posters

40 | 48 |

Teaching Assistantship Requirements Completed

49 | 58 |

Additional Courses

59 | 67 |

Additional Workshops & Conferences

68 | 75 |

Extracurricular

76 | 88 |

Since my last committee meeting:

89 |

AIM 1 To identify and characterize parent of origin effects on quantitative traits in the Hutterites.
90 | Completed with preprint on bioRxiv (Mozaffari et al. 2017), working on revising and resubmitting. We are working on replicating the significant opposite effects of SNPs.

91 |


92 | AIM 2a To identify and characterize parent of origin effects on gene expression in 306 Hutterites.
93 | Manuscript draft on imprinted genes identified in LCLs completed. Includes replication of genes in whole blood gene expression and whole blood methylation.

94 |


95 | AIM 2b To identify and characterize parent of origin and allele specific effects on gene expression in 306 Hutterites.
96 | I first performed opposite effect POeQTLs (similar method as in Aim 1) on total LCL gene expression. We subsetted on SNPs with at least three individuals in at least three genotype groups (out of four if you call parent of origin) and found no significant associations (Bonferonni p-value cutoff 1e-07).
97 | I then tested maternally inherited SNPs with the maternal gene expression and paternally inherited SNPs with paternal expression in cis. I’ll share results at the meeting.
98 |

99 |
100 |
101 |

Mozaffari, S V, J M DeCara, S J Shah, R M Lang, Dan L Nicolae, and Carole Ober. 2017. “Parent of Origin Effects on Quantitative Phenotypes in a Founder Population.” bioRxiv.

102 |
103 |
104 | -------------------------------------------------------------------------------- /2018/main.tex: -------------------------------------------------------------------------------- 1 | \documentclass[a4paper, 11pt]{article} 2 | \usepackage{comment} % enables the use of multi-line comments (\ifx \fi) 3 | \usepackage{fullpage} % changes the margin 4 | \usepackage[margin=35pt]{geometry} 5 | \usepackage{graphicx} 6 | \usepackage{microtype} 7 | \usepackage{titlesec} 8 | \usepackage{color, colortbl} 9 | \usepackage[table]{xcolor} 10 | \usepackage[numbers,super]{natbib} 11 | \usepackage{bibentry} 12 | \nobibliography* 13 | 14 | %\usepackage[most]{tcolorbox} 15 | 16 | %\usepackage{fontspec} 17 | %\setmainfont{Georgia} 18 | \titleformat*{\section}{\large\bfseries} 19 | 20 | \begin{document} 21 | 22 | \noindent 23 | \large\textbf{Committee Meeting Report} \hfill \textbf{Sahar Mozaffari} \\ 24 | \normalsize \hfill Professor: Carole Ober \\ 25 | GGSB Matriculated 2013 \hfill Date: 3/8/18 \\ 26 | \noindent\makebox[\linewidth]{\rule{\paperwidth}{0.4pt}} 27 | 28 | \large\textbf{\\Progress since last Committee Meeting - October 2, 2017} 29 | \subsection*{Awards} 30 | % Horizontal line after name; adjust line thickness by changing the '1pt' 31 | \begin{itemize} 32 | \item ASHG Reviewer's Choice Abstract Award \hfill 2016 \& 2017 33 | \item Awarded \& Renewed F31 Ruth L. Kirschstein NRSA \hfill 9/2016-9/2018 34 | \item FASEB MARC Travel Award to ASHG \hfill 2014 \& 2015 35 | \item Genetics and Regulation Training Grant \hfill 2013-2016 36 | \end{itemize} 37 | 38 | \subsection*{Manuscripts in progress} 39 | \begin{itemize} 40 | \item Submitting: \bibentry{Mozaffari:loXwTR9q} 41 | \item Revising: \bibentry{Mozaffari:dg} 42 | \item Submitted: \bibentry{Shiquan:G-C-HqrA} 43 | \end{itemize} 44 | 45 | \subsection*{Published} 46 | \begin{itemize} 47 | \item \bibentry{Hart:2018cv} 48 | \item \bibentry{Igartua:2017ir} 49 | \item \bibentry{Gamazon:2015fa} 50 | \end{itemize} 51 | 52 | \subsection*{Oral Presentations} 53 | \begin{itemize} 54 | \item GGSB Work in Progress \hfill April 2016 \& March 2017\\ \emph{Parent of Origin Effects in the Hutterites} 55 | \item Genetics of Model Organisms Club \hfill April 21, 2016\\ \emph{Parent of Origin Effects in the Hutterites} 56 | \item Human Genetics Work in Progress \hfill January 20, 2016\\ \emph{Parent of Origin Effects} 57 | \item Molecular Biosciences Retreat \hfill November 5, 2015\\ Mozaffari SV, DeCara J, Shah S, Herman C, Lang R, Nicolae D, Ober C., \emph{Parent of Origin GWAS with Cardiovascular Disease Associated Traits in the Hutterites.} 2015: Nov 5; Galena, IL. 58 | \item ASHG\hfill October 9, 2015\\ Mozaffari SV, DeCara J, Shah S, Herman C, Lang R, Nicolae D, Ober C., \emph{Parent of Origin GWAS of CVD-Associated Phenotypes in the Hutterites} (Abstract Program \#310). Presented at the Annual Meeting of The American Society of Human Genetics; 2015: Oct 9; Baltimore, MD. 59 | 60 | 61 | \end{itemize} 62 | 63 | \subsection*{Posters} 64 | \begin{itemize} 65 | \item Reviewer's Choice Abstract Award: \\Mozaffari SV, Nicolae D, Ober C. Identifying Imprinted Genes and Parent of Origin Effects on Gene Expression in the Hutterites. Poster presented at the Annual Meeting of The American Society of Human Genetics Conference; 2017: Oct 17-21; Orlando, FL 66 | \item Mozaffari SV, Nicolae D, Ober C. \emph{Opposite Allele Parent of Origin Effects on Cardiovascular and Asthma Associated Traits in the Hutterites}. Poster presented at the Gordon Research Seminar and Conference; 2017: July 8-14; Stowe, VT 67 | \item Reviewer's Choice Abstract Award: \\Mozaffari SV, Nicolae D, Ober C. Opposite Allele Parent of Origin Effects on Body Mass Index in the Hutterites. Poster presented at the Annual Meeting of The American Society of Human Genetics Conference; 2016: Oct 18-22; Vancouver, Canada 68 | \item Mozaffari SV, Gamazon E, Aquino-Michaels K, Cox NJ, Im HK. \emph{Quantifying Context Specificity of Gene Regulation using Predicted Gene Expression Levels.} Poster presented at the Annual Meeting of The American Society of Human Genetics Conference; 2014: Oct 18-22; San Diego, CA 69 | 70 | \end{itemize} 71 | 72 | \subsection*{Teaching Assistantship Requirements Completed} 73 | \begin{itemize} 74 | \item BIOS 20187 \emph{Fundamentals of Genetics} \hfill Winter 2018\\ 75 | - Undergraduate Course: Recent developments in molecular genetics and the human genome project integrated into the structure of classical genetics. 76 | \item HGEN 47000 \emph{Human Genetics} \hfill Fall 2015 \& 2017\\ 77 | - Graduate Course: Classic and modern approaches to studying cytogenetic, Mendelian, and complex human diseases. Grant proposal writing course. \\ - Fall 2017: Conducting two-day computational workshop on GWAS 78 | \item MGCB 31400 (BIOS 21236) \emph{Genetic Analysis of Model Organisms}\hfill Fall 2014\\ 79 | - Graduate \& Undergraduate Course: Introduction to genetic tools, experiments, and model organisms 80 | \end{itemize} 81 | 82 | 83 | 84 | \subsection*{Additional Courses} 85 | \begin{itemize} 86 | \item STAT 24500 \emph{Statistical Theory \& Methods II }\hfill Winter 2015 87 | \item HGEN 46900 \emph{Human Variation \& Disease} \hfill Spring 2015 88 | \item STAT 35500 \emph{Statistical Genetics} \hfill Spring 2015 89 | \item myChoice Mini-Course: \emph{Effective Writing in the Biological Sciences} \hfill Fall 2015 90 | \item HGEN 48600 \emph{Fundamentals of Computational Biology: Models \& Inference} \hfill Winter 2016 91 | \item PBHS 31831 \emph{Genetic \& Molecular Epidemiology} \hfill Spring 2016 92 | 93 | 94 | \end{itemize} 95 | 96 | \subsection*{Additional Workshops \& Conferences} 97 | \begin{itemize} 98 | \item ComSciCon Chicago (Communicating Science Conference \& Workshop) \hfill August 2017 99 | \item Gordon Research Seminar \& Conference: Human Genetics \& Genomics \hfill July 2017 \\ Discussion Leader for mentorship session at GRS 100 | \item Summer Institute in Statistical Genetics at the University of Washington \hfill July 2016 101 | \item Master R Developer Workshop taught by Hadley Wickham \hfill May 2015 102 | \end{itemize} 103 | 104 | \subsection*{Extracurricular} 105 | \begin{itemize} 106 | \item Museum of Science \& Industry: Science Connections volunteer \hfill Fall 2014-current \\ 107 | Introduce genetic concepts to guests in a fun and engaging way, incorporating hands-on activities.\\Assist in the Fabrication Lab helping guests design and print custom objects using 3D printers and laser cutters. 108 | 109 | \item myCHOICE Data Science Trek to San Francisco Bay Area \hfill November 2017 \\ 110 | Visit PhD alumns at 23andMe, Genentech, Ancestry, Illumina, Genomic Health, etc. 111 | \item UChicago Software Carpentry Helper \hfill Fall 2015, 2016, \& 2017 112 | \item Expanding Your Horizons (EYH) Chicago: volunteer \hfill March 2017 \\ 113 | Engage, inspire, and empower young girls to pursue STEM careers at a one-day STEM symposium where 300 middle school girls participate in hands-on science, technology, engineering and math led by academic and professional women. 114 | \item myCHOICE Internship: Institute of Translational Medicine: writer \hfill Summer 2015\\Translate complex research into dynamic science stories. Share translational research stories in weekly newsletter, ITM website, and social media platforms 115 | 116 | \end{itemize} 117 | 118 | 119 | 120 | %\noindent\makebox[\linewidth]{\rule{\paperwidth}{0.4pt}} 121 | 122 | %\section*{Attachments} 123 | %Make sure to change these 124 | %Lab Notes, HelloWorld.ic, FooBar.ic 125 | %\fi %comment me out 126 | \newpage 127 | 128 | %\noindent\makebox[\linewidth]{\rule{\paperwidth}{0.4pt}} 129 | \section*{Since my last committee meeting:} %\begin{tcolorbox}[colback=white,colframe=red!75!black] 130 | \textbf{AIM 1} To identify and characterize parent of origin effects on quantitative traits in the Hutterites. \\ 131 | 132 | Completed with preprint on bioRxiv \cite{Mozaffari:dg}, working on revising and resubmitting. We are working on replicating the significant opposite effects of SNPs. 133 | 134 | \textbf{\\AIM 2a} To identify and characterize parent of origin effects on gene expression in 306 Hutterites.\\ 135 | 136 | Manuscript draft on imprinted genes identified in LCLs completed. Includes replication of genes in whole blood gene expression and whole blood methylation. 137 | 138 | \textbf{\\AIM 2b} To identify and characterize parent of origin and allele specific effects on gene expression in 306 Hutterites.\\ 139 | 140 | I first performed opposite effect POeQTLs (similar method as in Aim 1) on total LCL gene expression. We subsetted on SNPs with at least three individuals in at least three genotype groups (out of four if you call parent of origin) and found no significant associations (Bonferonni p-value cutoff 1e-07).\\ 141 | 142 | I then tested maternally inherited SNPs with the maternal gene expression and paternally inherited SNPs with paternal expression in \textit{cis}. I'll share results at the meeting. \\ 143 | 144 | 145 | 146 | %\end{tcolorbox} 147 | \bibliography{report2018} 148 | \bibliographystyle{apalike} 149 | 150 | %\begin{thebibliography}{9} 151 | %\bibitem{Gamazon} Gamazon, E. R., Wheeler, H. E., Shah, K. P., Mozaffari, S. V., Aquino-Michaels, K., Carroll, R. J., et al. (2015). A gene-based association method for mapping traits using reference transcriptome data. Nature Genetics, 47(9), 1091–1098. http://doi.org/10.1038/ng.3367 152 | %\bibitem{Cusanovich} Cusanovich, D. A., Caliskan, M., Billstrand, C., Michelini, K., Chavarria, C., De Leon, S., et al. (2016). Integrated analyses of gene expression and genetic association studies in a founder population. Human Molecular Genetics, ddw061. http://doi.org/10.1093/hmg/ddw061 153 | %\bibitem{Dobin} Dobin, A., \& Gingeras, T. R. (2015). Mapping RNA-seq Reads with STAR. Current Protocols in Bioinformatics. 51, 11.14.1–19. http://doi.org/10.1002/0471250953.bi1114s51 154 | %\bibitem{Jun} G. Jun, M. Flickinger, K. N. Hetrick, Kurt, J. M. Romm, K. F. Doheny, G. Abecasis, M. Boehnke,and H. M. Kang, (2012) Detecting and Estimating Contamination of Human DNA Samples in Sequencing and Array-Based Genotype Data, AJHG doi:10.1016/j.ajhg.2012.09.004 (volume 91 issue 5 pp.839 - 848) 155 | %\bibitem{van de Geijn}van de Geijn B, McVicker G, Gilad Y, Pritchard JK. (2015) WASP: allele-specific software for robust molecular quantitative trait locus discovery. Nat Meth. 12:1061-1063. doi:10.1038/nmeth.3582. 156 | %\end{thebibliography} 157 | 158 | \end{document} 159 | -------------------------------------------------------------------------------- /2016/main.doc: -------------------------------------------------------------------------------- 1 |

Committee Meeting Report Sahar Mozaffari
2 | Professor: Carole Ober
3 | GGSB Matriculated 2013 Date: 09/08/16
4 |

5 |


6 | Progress since last Committee Meeting - June 16, 2015

7 |

Awards

8 | 14 |

Publications

15 | 18 |

Presentations

19 | 31 |

Posters

32 | 35 |

Teaching Assistantship Requirements Completed

36 | 42 |

Additional Courses

43 | 51 |

Additional Workshops

52 | 56 |

Extracurricular

57 | 62 |

Proposal Updates:

63 |

I would like to revise my aims to focus on Parent of Origin Effects. There are many different aspects of the project to explore and I would like to take advantage of it. These were my previous aims.

64 |


65 | AIM 1 To identify and characterize parent of origin effects and allele specific effects on gene expression in 430 Hutterites.
66 | AIM 2 To investigate association of gene age and eQTLs in endometrial-expressed genes in humans.
67 | AIM 3 To characterize the contributions of genetic variants, IBD segments, parent of origin, functional variants, and relatedness among individuals to predict clinical phenotypes.
68 | The following are my proposed revised aims:

69 |


70 | AIM 1a To identify and characterize parent of origin effects on quantitative traits in the Hutterites.
71 | AIM 1b To estimate maternal and paternal heritability measures on quantitative traits in the Hutterites.
72 | AIM 2a To identify and characterize parent of origin effects on gene expression in 430 Hutterites.
73 | AIM 2b To identify and characterize parent of origin and allele specific effects on gene expression in 430 Hutterites.
74 | Previously, I shared results on parent of effects on gene expression where I tested maternally- and paternally- inherited alleles separately with the sum of gene expression. I received feedback to separate the gene expression into reads that map maternally and those that map paternally, and to use these measures for POeQTL.

75 |


76 | Since my Qualifying Exam

77 |


78 | AIM 1
79 | I have ran Parent of Origin GWAS, testing maternally and paternally- inherited alleles separately with 22 different traits. The manhattan plots for the Maternal and Paternal GWAS for LDL are in Figure 1. Table 1 has the phenotypes with significant maternal and paternal allele associations.
80 |

81 |

[fig:POGWAS]Paternal and Maternal allele PO- GWAS Manhattan plots for LDL. [fig:POGWAS]Paternal and Maternal allele PO- GWAS Manhattan plots for LDL.

82 | 83 | 84 | 85 | 86 | 87 | 88 | 89 | 90 | 91 | 92 | 93 | 94 | 95 | 96 | 97 | 98 | 99 | 100 | 101 | 102 | 103 | 104 | 105 | 106 | 107 | 108 | 109 | 110 | 111 | 112 | 113 | 114 | 115 | 116 | 117 | 118 | 119 | 120 | 121 | 122 | 123 | 124 | 125 | 126 | 127 | 128 |
[tab:Signif]Phenotypes with Significant Maternal or Paternal Allele Associations.
Phenotypes
Significant Maternal AssociationCarotid Intima Media Thickness, FEV1, Trigylcerides
Significant Paternal AssociationsSystolic Blood Pressure, Blood eosinophil count LDL-C
Total cholesterol
No Significant Parental AssociationsLeft Atrial Volume Index, Left Ventricular Mass Index, FEV1/FVC,
Bronchial Responsiveness Index, Fraction exhaled nitric oxide
Diastolic Blood Pressure, Lymphocyte Count, Monocyte Count,
Neutrophil Count, IgE, Chitin, YKL40, BMI, Height, HDL-C  
129 |

I have also ran a new model (equation 1) that tests for difference of parental effects in two of these phenotypes (LDL & BMI), and I am working on running them on the remaining 20 phenotypes. I am working on replicating the interesting findings with BMI in the Framingham cohort.
130 |
$$\label{my_first_eqn} 131 | Y=\mu + (\beta_p-\beta_m)\frac{(X_p-X_m)}{2} +\frac{(\beta_p+\beta_m)}{2}X_{mp} + \epsilon$$
AIM 1b
132 | With the help of Mark Abney, I have models to test for parent of origin heritability. I have estimated the average maternal and average paternal heritability for each of the 22 traits and I am working on getting a more accurate measure (as opposed to average).
133 |
134 | AIM 2a
135 | I have remapped the LCL RNA-seq data using STAR and corrected sample swaps using verifyBamID (fixed 2 samples that were already included, and gained 4 samples). I used WASP to remove mapping bias and mapped reads to the maternal and paternal haplotypes.
136 |
137 | For this aim I have methods to detect patterns of parent of origin effects (i.e. imprinting) using maternal and paternal gene expression but not any SNPs (no POeQTL). First I test for asymmetry in maternal and paternal gene expression (normalized total gene expression) with permutations of the data. The second test uses a binomial test to get a Z-score of maternal and paternal expression within each sample (not normalized gene expression). The distribution of the Z-score can be tested against a normal distribution with the Shapiro-Wilk test. The most significant genes from this test have a lot of overlap with known imprinted genes as shown in Table 2 & 3.

138 |

AIM 2b
139 | I will test for POeQTLs in this aim testing maternally inherited SNPs with the maternal gene expression and paternally inherited SNPs with paternal expression. I will combine this with POeQTL results from before using the sum of gene expression, especially for genes which we don’t have maternal or paternal expression.

140 |

9 Gamazon, E. R., Wheeler, H. E., Shah, K. P., Mozaffari, S. V., Aquino-Michaels, K., Carroll, R. J., et al. (2015). A gene-based association method for mapping traits using reference transcriptome data. Nature Genetics, 47(9), 1091–1098. http://doi.org/10.1038/ng.3367 Cusanovich, D. A., Caliskan, M., Billstrand, C., Michelini, K., Chavarria, C., De Leon, S., et al. (2016). Integrated analyses of gene expression and genetic association studies in a founder population. Human Molecular Genetics, ddw061. http://doi.org/10.1093/hmg/ddw061 Dobin, A., & Gingeras, T. R. (2015). Mapping RNA-seq Reads with STAR. Current Protocols in Bioinformatics. 51, 11.14.1–19. http://doi.org/10.1002/0471250953.bi1114s51 G. Jun, M. Flickinger, K. N. Hetrick, Kurt, J. M. Romm, K. F. Doheny, G. Abecasis, M. Boehnke,and H. M. Kang, (2012) Detecting and Estimating Contamination of Human DNA Samples in Sequencing and Array-Based Genotype Data, AJHG doi:10.1016/j.ajhg.2012.09.004 (volume 91 issue 5 pp.839 - 848) van de Geijn B, McVicker G, Gilad Y, Pritchard JK. (2015) WASP: allele-specific software for robust molecular quantitative trait locus discovery. Nat Meth. 12:1061-1063. doi:10.1038/nmeth.3582.

141 | -------------------------------------------------------------------------------- /2017/main.tex: -------------------------------------------------------------------------------- 1 | \documentclass[a4paper, 11pt]{article} 2 | \usepackage{comment} % enables the use of multi-line comments (\ifx \fi) 3 | \usepackage{fullpage} % changes the margin 4 | \usepackage[margin=35pt]{geometry} 5 | \usepackage{graphicx} 6 | \usepackage{microtype} 7 | \usepackage{titlesec} 8 | \usepackage{color, colortbl} 9 | \usepackage[table]{xcolor} 10 | \usepackage[numbers,super]{natbib} 11 | \usepackage{bibentry} 12 | \nobibliography* 13 | 14 | %\usepackage[most]{tcolorbox} 15 | 16 | %\usepackage{fontspec} 17 | %\setmainfont{Georgia} 18 | \titleformat*{\section}{\large\bfseries} 19 | 20 | \begin{document} 21 | 22 | \noindent 23 | \large\textbf{Committee Meeting Report} \hfill \textbf{Sahar Mozaffari} \\ 24 | \normalsize \hfill Professor: Carole Ober \\ 25 | GGSB Matriculated 2013 \hfill Date: 10/02/17 \\ 26 | \noindent\makebox[\linewidth]{\rule{\paperwidth}{0.4pt}} 27 | 28 | \large\textbf{\\Progress since last Committee Meeting - September 8, 2016} 29 | \subsection*{Awards} 30 | % Horizontal line after name; adjust line thickness by changing the '1pt' 31 | \begin{itemize} 32 | \item ASHG Reviewer's Choice Abstract Award \hfill 2016 \& 2017 33 | \item Awarded \& Renewed F31 Ruth L. Kirschstein NRSA \hfill 9/2016-9/2018 34 | \item FASEB MARC Travel Award to ASHG \hfill 2014 \& 2015 35 | \item Genetics and Regulation Training Grant \hfill 2013-2016 36 | \end{itemize} 37 | 38 | \subsection*{Publications} 39 | \begin{itemize} 40 | \item Submitted to PeerJ: \bibentry{Hart:2017vg} 41 | \item Revising: \bibentry{Mozaffari:dg} 42 | \item Under revision Scientific Reports: \bibentry{Igartua:2017fg} 43 | \item \bibentry{Gamazon:2015fa} 44 | \end{itemize} 45 | 46 | \subsection*{Oral Presentations} 47 | \begin{itemize} 48 | \item GGSB Work in Progress \hfill April 2016 \& March 2017\\ \emph{Parent of Origin Effects in the Hutterites} 49 | % \item Genetics of Model Organisms Club \hfill April 21, 2016\\ \emph{Parent of Origin Effects in the Hutterites} 50 | \item Human Genetics Work in Progress \hfill January 20, 2016\\ \emph{Parent of Origin Effects} 51 | \item Molecular Biosciences Retreat \hfill November 5, 2015\\ Mozaffari SV, DeCara J, Shah S, Herman C, Lang R, Nicolae D, Ober C., \emph{Parent of Origin GWAS with Cardiovascular Disease Associated Traits in the Hutterites.} 2015: Nov 5; Galena, IL. 52 | \item ASHG\hfill October 9, 2015\\ Mozaffari SV, DeCara J, Shah S, Herman C, Lang R, Nicolae D, Ober C., \emph{Parent of Origin GWAS of CVD-Associated Phenotypes in the Hutterites} (Abstract Program \#310). Presented at the Annual Meeting of The American Society of Human Genetics; 2015: Oct 9; Baltimore, MD. 53 | 54 | 55 | \end{itemize} 56 | 57 | \subsection*{Posters} 58 | \begin{itemize} 59 | \item Mozaffari SV, Nicolae D, Ober C. \emph{Opposite Allele Parent of Origin Effects on Cardiovascular and Asthma Associated Traits in the Hutterites}. Poster presented at the Gordon Research Seminar and Conference; 2017: July 8-14; Stowe, VT 60 | \item Reviewer's Choice Abstract Award: \\Mozaffari SV, Nicolae D, Ober C. Opposite Allele Parent of Origin Effects on Body Mass Index in the Hutterites. Poster presented at the Annual Meeting of The American Society of Human Genetics Conference; 2016: Oct 18-22; Vancouver, Canada 61 | \item Mozaffari SV, Gamazon E, Aquino-Michaels K, Cox NJ, Im HK. \emph{Quantifying Context Specificity of Gene Regulation using Predicted Gene Expression Levels.} Poster presented at the Annual Meeting of The American Society of Human Genetics Conference; 2014: Oct 18-22; San Diego, CA 62 | 63 | \end{itemize} 64 | 65 | \subsection*{Teaching Assistantship Requirements Completed} 66 | \begin{itemize} 67 | \item HGEN 47000 \emph{Human Genetics} \hfill Fall 2015 \& 2017\\ 68 | - Graduate Course: Classic and modern approaches to studying cytogenetic, Mendelian, and complex human diseases. Grant proposal writing course. \\ - Fall 2017: Conducting two-day computational workshop on GWAS 69 | \item MGCB 31400 (BIOS 21236) \emph{Genetic Analysis of Model Organisms}\hfill Fall 2014\\ 70 | - Graduate \& Undergraduate Course: Introduction to genetic tools, experiments, and model organisms 71 | \end{itemize} 72 | 73 | 74 | 75 | \subsection*{Additional Courses} 76 | \begin{itemize} 77 | \item STAT 24500 \emph{Statistical Theory \& Methods II }\hfill Winter 2015 78 | \item HGEN 46900 \emph{Human Variation \& Disease} \hfill Spring 2015 79 | \item STAT 35500 \emph{Statistical Genetics} \hfill Spring 2015 80 | \item myChoice Mini-Course: \emph{Effective Writing in the Biological Sciences} \hfill Fall 2015 81 | \item HGEN 48600 \emph{Fundamentals of Computational Biology: Models \& Inference} \hfill Winter 2016 82 | \item PBHS 31831 \emph{Genetic \& Molecular Epidemiology} \hfill Spring 2016 83 | 84 | 85 | \end{itemize} 86 | 87 | \subsection*{Additional Workshops \& Conferences} 88 | \begin{itemize} 89 | \item ComSciCon Chicago (Communicating Science Conference \& Workshop) \hfill August 2017 90 | \item Gordon Research Seminar \& Conference: Human Genetics \& Genomics \hfill July 2017 \\ Discussion Leader for mentorship session at GRS 91 | \item Summer Institute in Statistical Genetics at the University of Washington \hfill July 2016 92 | \item Master R Developer Workshop taught by Hadley Wickham \hfill May 2015 93 | \end{itemize} 94 | 95 | \subsection*{Extracurricular} 96 | \begin{itemize} 97 | \item myCHOICE Data Science Trek to San Francisco Bay Area \hfill November 2017 98 | \item Museum of Science \& Industry: Science Connections volunteer \hfill Fall 2014-current \\ 99 | Introduce genetic concepts to guests in a fun and engaging way, incorporating hands-on activities.\\Assist in the Fabrication Lab helping guests design and print custom objects using 3D printers and laser cutters. 100 | \item UChicago Software Carpentry Helper \hfill Fall 2015, 2016, \& 2017 101 | \item Expanding Your Horizons (EYH) Chicago: volunteer \hfill March 2017 \\ 102 | Engage, inspire, and empower young girls to pursue STEM careers at a one-day STEM symposium where 300 middle school girls participate in hands-on science, technology, engineering and math led by academic and professional women. 103 | \item myCHOICE Internship: Institute of Translational Medicine: writer \hfill Summer 2015\\Translate complex research into dynamic science stories. Share translational research stories in weekly newsletter, ITM website, and social media platforms 104 | 105 | \end{itemize} 106 | 107 | 108 | 109 | %\noindent\makebox[\linewidth]{\rule{\paperwidth}{0.4pt}} 110 | 111 | %\section*{Attachments} 112 | %Make sure to change these 113 | %Lab Notes, HelloWorld.ic, FooBar.ic 114 | %\fi %comment me out 115 | \newpage 116 | 117 | %\noindent\makebox[\linewidth]{\rule{\paperwidth}{0.4pt}} 118 | \section*{Proposal Updates:} %\begin{tcolorbox}[colback=white,colframe=red!75!black] 119 | \textbf{AIM 1a} To identify and characterize parent of origin effects on quantitative traits in the Hutterites. 120 | \textbf{\\AIM 1b} To estimate maternal and paternal heritability measures on quantitative traits in the Hutterites.\\ 121 | \textbf{\\AIM 2a} To identify and characterize parent of origin effects on gene expression in 430 Hutterites.\\ 122 | \textbf{AIM 2b} To identify and characterize parent of origin and allele specific effects on gene expression in 430 Hutterites.\\ 123 | \textbf{\\Since my last Committee Meetng} 124 | \textbf{\\AIM 1a}\\ 125 | Completed with preprint on bioRxiv \cite{Mozaffari:dg}, working on revising and resubmitting. We are trying to replicate the significant opposite effects of SNPs in birth weight in the Hutterites. 126 | \textbf{\\AIM 1b}\\ 127 | Currently working on, adapting methods published in Mott \emph{et al.} \cite{Mott2014}. Last committee meeting, it was established this would be the last aim I work on . 128 | %\begin{figure}[!h] 129 | %\includegraphics[width=0.5\textwidth]{Manhattan_paternal_LDL_8_17_16.png} 130 | %\includegraphics[width=0.5\textwidth]{Manhattan_maternal_LDL_8_17_16.png} 131 | %\caption{\label{fig:POGWAS}Paternal and Maternal allele PO- GWAS Manhattan plots for LDL.} 132 | %\end{figure} 133 | 134 | \textbf{\\AIM 2a}\\ 135 | I have remapped the LCL RNA-seq data (and whole blood data for replication) using STAR\cite{Dobin:2012fg} and corrected sample swaps using verifyBamID.\cite{Jun:2012je} I used WASP\cite{vandeGeijn:2015hi} to remove mapping bias and remove duplicate reads. I then mapped reads to the maternal ($Y_m$) and paternal ($Y_p$) haplotypes. I used STAR to measure gene count from reads. I removed lowly expressed genes but did not normalize gene expression or remove covariates since comparing maternal and paternal expression is done in the same sample under the same conditions. \\ 136 | \\For this aim I am using simple binomial tests to detect patterns of parent of origin effects (i.e. imprinting) using maternal and paternal gene expression but not any SNPs (no POeQTL). (Removed duplicate reads so no need to model overdispersion). 137 | First, I can test for directional asymmetry to test if any genes have maternal or paternal effects by generating a binomial Z-score for each subject for each gene. I only use individuals where $Y_p+Y_m=5 $ and $Z_i \neq 0 $ to get a statistic of how skewed the gene expression is for each gene using a binomial test. 138 | \begin{equation}\label{Zscore} 139 | Z_i= \frac{(Y_p^{i}-Y_m^{i})}{\sqrt(Y_p^{i}+Y_m^{i})} 140 | \end{equation} 141 | \begin{equation}\label{signtest} 142 | S \sim Bin(\# subjects, \frac{1}{2}) 143 | \end{equation} 144 | 145 | Second, I test for asymmetry in maternal and paternal gene expression by genes and weighing by library size where $w_i \propto \frac{1}{library size_i} $ and $ w_i = \frac{10millionreads}{\#ofreads_i} $\\ 146 | \begin{equation}\label{my_first_eqn} 147 | Z_g= \frac{\sum_{i=1}^{n}w_i(Y_p^{i}-Y_m^{i})}{\sqrt(\sum_{i=1}^{n}w_i^2(Y_p^{i}+Y_m^{i}))} 148 | \end{equation} 149 | 150 | \begin{flushleft} 151 | \textbf{AIM 2b}\\ 152 | I will test for POeQTLs in this aim testing maternally inherited SNPs with the maternal gene expression and paternally inherited SNPs with paternal expression. I will combine this with POeQTL results from before using the sum of gene expression, especially for genes which we don't have maternal or paternal expression. 153 | 154 | \begin{equation}\label{poeqtl} 155 | Y_m \sim X_{SNP} + PO + PO\cdot X_{SNP} 156 | \end{equation} 157 | \begin{equation}\label{poeqtl_maternal} 158 | Y_p \sim X_{SNP} + PO + PO\cdot X_{SNP} 159 | \end{equation} 160 | 161 | \end{flushleft} 162 | 163 | 164 | \definecolor{lavender}{RGB}{230,230,250} 165 | \definecolor{mistyrose}{RGB}{255,228,225} 166 | 167 | \begin{table}[!ht] 168 | %\parbox{.45\linewidth}{ 169 | \begin{tabular}{c|c|c|c|c} 170 | Gene & Imprinted & Genepvalue & weighted Zscore & weighted pvalue \\ \hline 171 | 172 | \emph{ZDBF2} & yes & 7e\textsuperscript{-37} & 45.57 & 0 \\ \hline 173 | 174 | \emph{NHP2L1} & no, Docherty et al. \cite{Docherty:2014cx} & 7e\textsuperscript{-31} & 18.98 & 2e\textsuperscript{-80} \\ \hline 175 | 176 | \emph{L3MBTL1} & yes & 2e\textsuperscript{-29} & 35.73 & 1e\textsuperscript{-279} \\ \hline 177 | 178 | \emph{PEG10} & yes & 2e\textsuperscript{-29} & 51.34 & 0 \\ \hline 179 | 180 | \emph{SNHG14} & no, Baran et. al \cite{Baran:2015cx} & 8e\textsuperscript{-27} & 41.09 & 0 \\ \hline 181 | \emph{ZNF331} & no, Baran et. al \cite{Baran:2015cx} & 3e\textsuperscript{-23} & 30.28 & 2e\textsuperscript{-201} \\ \hline 182 | 183 | \emph{KCNQ1} & yes & 4e\textsuperscript{-21} & -28.94 & 4e\textsuperscript{-184}\\ \hline 184 | \emph{LPAR6} & no, Baran et. al \cite{Baran:2015cx} & 7e\textsuperscript{-21} & 33.50 & 4e\textsuperscript{-246}\\ \hline 185 | 186 | \emph{FAM50B} & yes & 4e\textsuperscript{-20} & 28.89 & 2e\textsuperscript{-183}\\ \hline 187 | \emph{PXDC1} & no, neighboring gene of FAM50B & 3e\textsuperscript{-14} & 16.05 & 6e\textsuperscript{-58}\\ \hline 188 | \emph{PWAR6} & no, Prader Willi/Angelman Region 6 & 1e\textsuperscript{-09} & 25.59 & 2e\textsuperscript{-144}\\ \hline 189 | 190 | \emph{NAP1L5} & yes & 3e\textsuperscript{-07} & 21.05 & 3e\textsuperscript{-98}\\ \hline 191 | \emph{ATP6V0D1} & no & 1e\textsuperscript{-06} & -5.40 & 7e\textsuperscript{-8}\\ \hline 192 | 193 | 194 | \end{tabular} 195 | \caption{\label{tab:Significant Genes} Significant genes from sign test (p-values in column 3) with weighted Z score with corresponding p-values in column 4 and 5, respectively. Imprinted as defined by geneimprint.com database. } 196 | %} 197 | \end{table} 198 | %\end{tcolorbox} 199 | \bibliography{report2017} 200 | \bibliographystyle{apalike} 201 | 202 | %\begin{thebibliography}{9} 203 | %\bibitem{Gamazon} Gamazon, E. R., Wheeler, H. E., Shah, K. P., Mozaffari, S. V., Aquino-Michaels, K., Carroll, R. J., et al. (2015). A gene-based association method for mapping traits using reference transcriptome data. Nature Genetics, 47(9), 1091–1098. http://doi.org/10.1038/ng.3367 204 | %\bibitem{Cusanovich} Cusanovich, D. A., Caliskan, M., Billstrand, C., Michelini, K., Chavarria, C., De Leon, S., et al. (2016). Integrated analyses of gene expression and genetic association studies in a founder population. Human Molecular Genetics, ddw061. http://doi.org/10.1093/hmg/ddw061 205 | %\bibitem{Dobin} Dobin, A., \& Gingeras, T. R. (2015). Mapping RNA-seq Reads with STAR. Current Protocols in Bioinformatics. 51, 11.14.1–19. http://doi.org/10.1002/0471250953.bi1114s51 206 | %\bibitem{Jun} G. Jun, M. Flickinger, K. N. Hetrick, Kurt, J. M. Romm, K. F. Doheny, G. Abecasis, M. Boehnke,and H. M. Kang, (2012) Detecting and Estimating Contamination of Human DNA Samples in Sequencing and Array-Based Genotype Data, AJHG doi:10.1016/j.ajhg.2012.09.004 (volume 91 issue 5 pp.839 - 848) 207 | %\bibitem{van de Geijn}van de Geijn B, McVicker G, Gilad Y, Pritchard JK. (2015) WASP: allele-specific software for robust molecular quantitative trait locus discovery. 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12 | %\usepackage{fontspec} 13 | %\setmainfont{Georgia} 14 | \titleformat*{\section}{\large\bfseries} 15 | 16 | \begin{document} 17 | 18 | \noindent 19 | \large\textbf{Committee Meeting Report} \hfill \textbf{Sahar Mozaffari} \\ 20 | \normalsize \hfill Professor: Carole Ober \\ 21 | GGSB Matriculated 2013 \hfill Date: 09/08/16 \\ 22 | \noindent\makebox[\linewidth]{\rule{\paperwidth}{0.4pt}} 23 | 24 | \large\textbf{\\Progress since last Committee Meeting - June 16, 2015} 25 | \subsection*{Awards} 26 | % Horizontal line after name; adjust line thickness by changing the '1pt' 27 | \begin{itemize} 28 | \item Awarded F31 Ruth L. Kirschstein NRSA 29 | \item FASEB MARC Travel Award to ASHG 2015 in Baltimore, MD 30 | \item FASEB MARC Travel Award to ASHG 2014 in San Diego, CA 31 | \item Genetics and Regulation Training Grant: 2013-2016 32 | \end{itemize} 33 | 34 | \subsection*{Publications} 35 | \begin{itemize} 36 | \item Gamazon, E. R., Wheeler, H. E., Shah, K. P., Mozaffari, S. V., Aquino-Michaels, K., Carroll, R. J., et al. (2015). \emph{A gene-based association method for mapping traits using reference transcriptome data.} Nature Genetics, 47(9), 1091–1098. http://doi.org/10.1038/ng.3367\cite{Gamazon} 37 | \end{itemize} 38 | 39 | \subsection*{Presentations} 40 | \begin{itemize} 41 | \item Genetics of Model Organisms Club \hfill April 21, 2016\\ 42 | Mozaffari, SV. \emph{Parent of Origin Effects in the Hutterites} 43 | \item Complex Trait Mapping Journal Club \hfill March 25, 2016\\ 44 | Paper: Amin V, Harris RA, Onuchic V, et al. \emph{Epigenomic footprints across 111 reference epigenomes reveal tissue-specific epigenetic regulation of lincRNAs.} Nat Commun. 2015;6:6370. 45 | \item Human Genetics Work in Progress \hfill January 20, 2016\\ 46 | Mozaffari, SV. \emph{Parent of Origin Effects} 47 | \item Molecular Biosciences Retreat \hfill November 5, 2015\\ Mozaffari SV, DeCara J, Shah S, Herman C, Lang R, Nicolae D, Ober C., \emph{Parent of Origin GWAS with Cardiovascular Disease Associated Traits in the Hutterites.} 2015: Nov 5; Galena, IL. 48 | \item ASHG\hfill October 9, 2015\\ Mozaffari SV, DeCara J, Shah S, Herman C, Lang R, Nicolae D, Ober C., \emph{Parent of Origin GWAS of CVD-Associated Phenotypes in the Hutterites} (Abstract Program \#310). Presented at the Annual Meeting of The American Society of Human Genetics; 2015: Oct 9; Baltimore, MD. 49 | 50 | 51 | \end{itemize} 52 | 53 | \subsection*{Posters} 54 | \begin{itemize} 55 | \item Mozaffari SV, Gamazon E, Aquino-Michaels K, Cox NJ, Im HK. \emph{Quantifying Context Specificity of Gene Regulation using Predicted Gene Expression Levels.} Poster presented at the Annual Meeting of The American Society of Human Genetics Conference; 2014: Oct 18-22; San Diego, CA 56 | \end{itemize} 57 | 58 | \subsection*{Teaching Assistantship Requirements Completed} 59 | \begin{itemize} 60 | \item MGCB 31400 (BIOS 21236) \emph{Genetic Analysis of Model Organisms}\hfill Fall 2014\\ 61 | Graduate \& Undergraduate Course: Introduction to genetic tools, experiments, and model organisms 62 | 63 | \item HGEN 47000 \emph{Human Genetics} \hfill Fall 2015\\ 64 | Graduate Course: Classic and modern approaches to studying cytogenetic, Mendelian, and complex human diseases. Grant proposal writing course. 65 | \end{itemize} 66 | 67 | 68 | \subsection*{Additional Courses} 69 | \begin{itemize} 70 | \item STAT 24500 \emph{Statistical Theory \& Methods II }\hfill Winter 2015 71 | \item HGEN 46900 \emph{Human Variation \& Disease} \hfill Spring 2015 72 | \item STAT 35500 \emph{Statistical Genetics} \hfill Spring 2015 73 | \item myChoice Mini-Course: \emph{Effective Writing in the Biological Sciences} \hfill Fall 2015 74 | \item HGEN 48600 \emph{Fundamentals of Computational Biology: Models \& Inference} \hfill Winter 2016 75 | \item PBHS 31831 \emph{Genetic \& Molecular Epidemiology} \hfill Spring 2016 76 | 77 | 78 | \end{itemize} 79 | 80 | \subsection*{Additional Workshops} 81 | \begin{itemize} 82 | \item Master R Developer Workshop taught by Hadley Wickham \hfill May 2015 83 | \item Summer Institute in Statistical Genetics at the University of Washington \hfill July 2016 84 | \end{itemize} 85 | 86 | \subsection*{Extracurricular} 87 | \begin{itemize} 88 | \item Museum of Science \& Industry: Science Connections volunteer \hfill Fall 2014-current 89 | \item myCHOICE Internship: Institute of Translational Medicine \hfill Summer 2015\\Translate complex research into dynamic science stories. Share translational research stories in weekly newsletter, ITM website, and social media platforms 90 | 91 | \end{itemize} 92 | 93 | 94 | 95 | %\noindent\makebox[\linewidth]{\rule{\paperwidth}{0.4pt}} 96 | 97 | %\section*{Attachments} 98 | %Make sure to change these 99 | %Lab Notes, HelloWorld.ic, FooBar.ic 100 | %\fi %comment me out 101 | \newpage 102 | 103 | %\noindent\makebox[\linewidth]{\rule{\paperwidth}{0.4pt}} 104 | \section*{Proposal Updates:} 105 | %\begin{tcolorbox}[colback=white,colframe=red!75!black] 106 | I would like to revise my aims to focus on Parent of Origin Effects. There are many different aspects of the project to explore and I would like to take advantage of it. These were my previous aims. 107 | 108 | \textbf{\\AIM 1} To identify and characterize parent of origin effects and allele specific effects on gene expression in 430 Hutterites.\\ 109 | \textbf{AIM 2} To investigate association of gene age and eQTLs in endometrial-expressed genes in humans.\\ 110 | \textbf{AIM 3} To characterize the contributions of genetic variants, IBD segments, parent of origin, functional variants, and relatedness among individuals to predict clinical phenotypes.\\ 111 | 112 | The following are my proposed revised aims: 113 | 114 | \textbf{\\AIM 1a} To identify and characterize parent of origin effects on quantitative traits in the Hutterites. 115 | \textbf{\\AIM 1b} To estimate maternal and paternal heritability measures on quantitative traits in the Hutterites. 116 | \textbf{\\AIM 2a} To identify and characterize parent of origin effects on gene expression in 430 Hutterites.\\ 117 | \textbf{AIM 2b} To identify and characterize parent of origin and allele specific effects on gene expression in 430 Hutterites.\\ 118 | 119 | 120 | 121 | Previously, I shared results on parent of effects on gene expression where I tested maternally- and paternally- inherited alleles separately with the sum of gene expression.\cite{Cusanovich} I received feedback to separate the gene expression into reads that map maternally and those that map paternally, and to use these measures for POeQTL. 122 | 123 | \textbf{\\Since my Qualifying Exam} 124 | 125 | \textbf{\\AIM 1}\\ 126 | I have ran Parent of Origin GWAS, testing maternally and paternally- inherited alleles separately with 22 different traits. The manhattan plots for the Maternal and Paternal GWAS for LDL are in Figure 1. Table 1 has the phenotypes with significant maternal and paternal allele associations. \\ 127 | 128 | \begin{figure}[!h] 129 | \includegraphics[width=0.5\textwidth]{Manhattan_paternal_LDL_8_17_16.png} 130 | \includegraphics[width=0.5\textwidth]{Manhattan_maternal_LDL_8_17_16.png} 131 | \caption{\label{fig:POGWAS}Paternal and Maternal allele PO- GWAS Manhattan plots for LDL.} 132 | \end{figure} 133 | 134 | \begin{table}[!h] 135 | \begin{centering} 136 | \begin{tabular}{lll} \hline 137 | & Phenotypes \\ \hline 138 | Significant Maternal Association & Carotid Intima Media Thickness, FEV\textsubscript{1}, Trigylcerides \\ \hline 139 | Significant Paternal Associations & Systolic Blood Pressure, Blood eosinophil count LDL-C \\ & Total cholesterol\\ \hline 140 | No Significant Parental Associations & Left Atrial Volume Index, Left Ventricular Mass Index, FEV\textsubscript{1}/FVC, \\ & Bronchial Responsiveness Index, Fraction exhaled nitric oxide \\ 141 | & Diastolic Blood Pressure, Lymphocyte Count, Monocyte Count, \\ 142 | & Neutrophil Count, IgE, Chitin, YKL40, BMI, Height, HDL-C \ \\ \hline 143 | \end{tabular} 144 | \caption{\label{tab:Signif}Phenotypes with Significant Maternal or Paternal Allele Associations.} 145 | \end{centering} 146 | \end{table} 147 | \newpage 148 | I have also ran a new model (equation 1) that tests for difference of parental effects in two of these phenotypes (LDL \& BMI), and I am working on running them on the remaining 20 phenotypes. I am working on replicating the interesting findings with BMI in the Framingham cohort.\\ 149 | \begin{equation}\label{my_first_eqn} 150 | Y=\mu + (\beta_p-\beta_m)\frac{(X_p-X_m)}{2} +\frac{(\beta_p+\beta_m)}{2}X_{mp} + \epsilon 151 | \end{equation} 152 | \textbf{AIM 1b}\\With the help of Mark Abney, I have models to test for parent of origin heritability. I have estimated the average maternal and average paternal heritability for each of the 22 traits and I am working on getting a more accurate measure (as opposed to average).\\ 153 | \textbf{\\AIM 2a}\\ 154 | I have remapped the LCL RNA-seq data using STAR\cite{Dobin} and corrected sample swaps using verifyBamID (fixed 2 samples that were already included, and gained 4 samples).\cite{Jun} I used WASP\cite{van de Geijn} to remove mapping bias and mapped reads to the maternal and paternal haplotypes.\\ 155 | \\For this aim I have methods to detect patterns of parent of origin effects (i.e. imprinting) using maternal and paternal gene expression but not any SNPs (no POeQTL). First I test for asymmetry in maternal and paternal gene expression (normalized total gene expression) with permutations of the data. The second test uses a binomial test to get a Z-score of maternal and paternal expression within each sample (not normalized gene expression). The distribution of the Z-score can be tested against a normal distribution with the Shapiro-Wilk test. The most significant genes from this test have a lot of overlap with known imprinted genes as shown in Table 2 \& 3. 156 | 157 | %\begin{table}[!h] 158 | %\begin{centering} 159 | %\begin{tabular}{l|l|l} 160 | %Predicted Paternally Imprinted & Imprinted & Shapiro-Wilk p-value \\ \hline 161 | %CACNA2D1 & no & \\ \hline 162 | %UNC93B1 & no & \\ \hline 163 | 164 | %\end{tabular} 165 | %\caption{\label{tab:Genes}Significant Genes that have Parent of Origin effects} 166 | %\quad 167 | %\end{centering} 168 | %\end{table} 169 | 170 | \definecolor{lavender}{RGB}{230,230,250} 171 | \definecolor{mistyrose}{RGB}{255,228,225} 172 | 173 | \begin{table}[!ht] 174 | \parbox{.45\linewidth}{ 175 | \begin{tabular}{l|lll} 176 | Gene & Imprinted & Asymmetry & Shapiro \\ \hline 177 | \emph{CACNA2} & no & 0 & 0.58 \\ \hline 178 | \emph{UNC93B1} & no & 0 & 0.72\\ \hline 179 | \emph{HCAR2} & no & 0 & NA\\ \hline 180 | \emph{CTAGE10} & no & 0 & 5e\textsuperscript{-08}\\ \hline 181 | \emph{MTRNR2} & no & 0 & 0.46\\ \hline 182 | \emph{CRYBB2P} & no & 0 & 0.18 \\ \hline 183 | \rowcolor{mistyrose} 184 | \emph{H19} & yes & 0 & 1.57e\textsuperscript{-08}\\ \hline 185 | \emph{SUPT4H1} & no & 0 & 0.75\\ \hline 186 | \emph{EIF4A3} & no & 0 & 0.14\\ \hline 187 | \rowcolor{mistyrose} 188 | \emph{ZNF597} & yes & 0 &5.63e\textsuperscript{-13}\\ \hline 189 | \emph{DIDO1} & no & 0 & 1.05e\textsuperscript{-03}\\ \hline 190 | \emph{EIF2AK1} & no & 0 & 0.12\\ \hline 191 | \emph{LOC38897} & no & 0 & 1.65e\textsuperscript{-08}\\ \hline 192 | \rowcolor{mistyrose} 193 | \emph{KCNQ1} & yes & 0 & 0 \\ \hline 194 | \emph{SEC61A1} & no & 0 & 2.43e\textsuperscript{-06}\\ \hline 195 | \emph{CPNE1} & no & 0 & 0\\ \hline 196 | \emph{SEC22B} & no & 0 & 0\\ \hline 197 | 198 | 199 | \end{tabular} 200 | \caption{\label{tab:PaternalGenes} Paternally Imprinted (maternally expressed) genes significant from the Asymmetry test (p-values in column 3); top 17 genes with p-value 0. Known imprinting status in column 2, and Shapiro test p-value in column 4. Colored in pink are known paternally imprinted genes from geneimprint.com.} 201 | } 202 | \quad 203 | \parbox{.45\linewidth}{ 204 | 205 | %\begin{centering} 206 | \begin{tabular}{l|lll} 207 | Gene & Imprinted & Asymmetry & Shapiro \\ \hline 208 | 209 | \rowcolor{lavender} 210 | \emph{MEST} & yes & 0 & 2.3e\textsuperscript{-07}\\ \hline 211 | 212 | \emph{MRPL28} & no & 0 & 0.13\\ \hline 213 | \rowcolor{lavender} 214 | \emph{BMP8A} & yes & 0 &3.67e\textsuperscript{-06}\\ \hline 215 | \emph{EIF5AL1} & no & 0 &0.08\\ \hline 216 | \rowcolor{lavender} 217 | \emph{FAM50B} & yes & 0 & 6.05e\textsuperscript{-12}\\ \hline 218 | \emph{PRIM2} & conflicting & 0 & 0.72\\ \hline 219 | \emph{TCEA1} & no & 0 & 0.02\\ \hline 220 | \emph{LPAR6} & no &0 & 3.65e\textsuperscript{-05}\\ \hline 221 | \emph{PCGF5} & no & 0 &2.18e\textsuperscript{-17}\\ \hline 222 | \emph{DUSP22} & no & 0 & 0.24\\ \hline 223 | \emph{ZNF331} & no & 0 & 0.24\\ \hline 224 | \rowcolor{lavender} 225 | \emph{NHP2L1} & yes & 0 & 3.13e\textsuperscript{-05}\\ \hline 226 | \rowcolor{lavender} 227 | \emph{ZDBF2} & yes & 0 &1.31e\textsuperscript{-09}\\ \hline 228 | \rowcolor{lavender} 229 | \emph{PEG10} & yes & 0 &2.29e\textsuperscript{-10}\\ \hline 230 | \emph{TMEM30A} & no & 0 & 0.98\\ \hline 231 | \emph{BCLAF1} & no & 0 &1.5e\textsuperscript{-04}\\ \hline 232 | \emph{MAP2K3} & no & 0 & 7.2e\textsuperscript{-13}\\ \hline 233 | \end{tabular} 234 | \caption{\label{tab:MaternalGenes} Maternally Imprinted (paternally expressed) genes significant from the Asymmetry test (p-values in column 3); top 17 genes with p-value 0. Known imprinting status in column 2, and Shapiro test p-value in column 4. Colored in blue are known maternally imprinted genes from geneimprint.com.} 235 | } 236 | \quad 237 | 238 | \end{table} 239 | \begin{flushleft} 240 | \textbf{AIM 2b}\\ 241 | I will test for POeQTLs in this aim testing maternally inherited SNPs with the maternal gene expression and paternally inherited SNPs with paternal expression. I will combine this with POeQTL results from before using the sum of gene expression, especially for genes which we don't have maternal or paternal expression. 242 | \end{flushleft} 243 | %\end{tcolorbox} 244 | \begin{thebibliography}{9} 245 | \bibitem{Gamazon} Gamazon, E. R., Wheeler, H. E., Shah, K. P., Mozaffari, S. V., Aquino-Michaels, K., Carroll, R. J., et al. (2015). A gene-based association method for mapping traits using reference transcriptome data. Nature Genetics, 47(9), 1091–1098. http://doi.org/10.1038/ng.3367 246 | \bibitem{Cusanovich} Cusanovich, D. A., Caliskan, M., Billstrand, C., Michelini, K., Chavarria, C., De Leon, S., et al. (2016). Integrated analyses of gene expression and genetic association studies in a founder population. Human Molecular Genetics, ddw061. http://doi.org/10.1093/hmg/ddw061 247 | \bibitem{Dobin} Dobin, A., \& Gingeras, T. R. (2015). Mapping RNA-seq Reads with STAR. Current Protocols in Bioinformatics. 51, 11.14.1–19. http://doi.org/10.1002/0471250953.bi1114s51 248 | \bibitem{Jun} G. Jun, M. Flickinger, K. N. Hetrick, Kurt, J. M. Romm, K. F. Doheny, G. Abecasis, M. Boehnke,and H. M. Kang, (2012) Detecting and Estimating Contamination of Human DNA Samples in Sequencing and Array-Based Genotype Data, AJHG doi:10.1016/j.ajhg.2012.09.004 (volume 91 issue 5 pp.839 - 848) 249 | \bibitem{van de Geijn}van de Geijn B, McVicker G, Gilad Y, Pritchard JK. (2015) WASP: allele-specific software for robust molecular quantitative trait locus discovery. Nat Meth. 12:1061-1063. doi:10.1038/nmeth.3582. 250 | \end{thebibliography} 251 | 252 | \end{document} 253 | -------------------------------------------------------------------------------- /2017/main.log: -------------------------------------------------------------------------------- 1 | This is pdfTeX, Version 3.14159265-2.6-1.40.18 (TeX Live 2017) (preloaded format=pdflatex 2017.5.23) 11 JUN 2018 13:21 2 | entering extended mode 3 | restricted \write18 enabled. 4 | file:line:error style messages enabled. 5 | %&-line parsing enabled. 6 | **main.tex 7 | (./main.tex 8 | LaTeX2e <2017-04-15> 9 | Babel <3.10> and hyphenation patterns for 84 language(s) loaded. 10 | (/usr/local/texlive/2017/texmf-dist/tex/latex/base/article.cls 11 | Document Class: article 2014/09/29 v1.4h Standard LaTeX document class 12 | (/usr/local/texlive/2017/texmf-dist/tex/latex/base/size11.clo 13 | File: size11.clo 2014/09/29 v1.4h Standard LaTeX file (size option) 14 | ) 15 | \c@part=\count79 16 | 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Committee Meeting Report Sahar Mozaffari
2 | Professor: Carole Ober
3 | GGSB Matriculated 2013 Date: 10/02/17
4 |

5 |


6 | Progress since last Committee Meeting - September 8, 2016

7 |

Awards

8 | 14 |

Publications

15 | 21 |

Oral Presentations

22 | 32 |

Posters

33 | 39 |

Teaching Assistantship Requirements Completed

40 | 47 |

Additional Courses

48 | 56 |

Additional Workshops & Conferences

57 | 64 |

Extracurricular

65 | 76 |

Proposal Updates:

77 |

AIM 1a To identify and characterize parent of origin effects on quantitative traits in the Hutterites.
78 | AIM 1b To estimate maternal and paternal heritability measures on quantitative traits in the Hutterites.
79 |
80 | AIM 2a To identify and characterize parent of origin effects on gene expression in 430 Hutterites.
81 | AIM 2b To identify and characterize parent of origin and allele specific effects on gene expression in 430 Hutterites.
82 |
83 | Since my last Committee Meetng
84 | AIM 1a
85 | Completed with preprint on bioRxiv (Mozaffari et al. 2017), working on revising and resubmitting. We are trying to replicate the significant opposite effects of SNPs in birth weight in the Hutterites.
86 | AIM 1b
87 | Currently working on, adapting methods published in Mott et al. (Mott et al. 2014). Last committee meeting, it was established this would be the last aim I work on .
88 | AIM 2a
89 | I have remapped the LCL RNA-seq data (and whole blood data for replication) using STAR(Dobin et al. 2012) and corrected sample swaps using verifyBamID.(Jun et al. 2012) I used WASP(Geijn et al. 2015) to remove mapping bias and remove duplicate reads. I then mapped reads to the maternal (Ym) and paternal (Yp) haplotypes. I used STAR to measure gene count from reads. I removed lowly expressed genes but did not normalize gene expression or remove covariates since comparing maternal and paternal expression is done in the same sample under the same conditions.
90 |
91 | For this aim I am using simple binomial tests to detect patterns of parent of origin effects (i.e. imprinting) using maternal and paternal gene expression but not any SNPs (no POeQTL). (Removed duplicate reads so no need to model overdispersion). First, I can test for directional asymmetry to test if any genes have maternal or paternal effects by generating a binomial Z-score for each subject for each gene. I only use individuals where Yp + Ym = 5 and Zi ≠ 0 to get a statistic of how skewed the gene expression is for each gene using a binomial test.
$$\label{Zscore} 92 | Z_i= \frac{(Y_p^{i}-Y_m^{i})}{\sqrt(Y_p^{i}+Y_m^{i})}$$

$$\label{signtest} 93 | S \sim Bin(\# subjects, \frac{1}{2})$$

94 |

Second, I test for asymmetry in maternal and paternal gene expression by genes and weighing by library size where $w_i \propto \frac{1}{library size_i} $ and $ w_i = \frac{10millionreads}{\#ofreads_i} $
95 |
$$\label{my_first_eqn} 96 | Z_g= \frac{\sum_{i=1}^{n}w_i(Y_p^{i}-Y_m^{i})}{\sqrt(\sum_{i=1}^{n}w_i^2(Y_p^{i}+Y_m^{i}))}$$

97 |

AIM 2b
98 | I will test for POeQTLs in this aim testing maternally inherited SNPs with the maternal gene expression and paternally inherited SNPs with paternal expression. I will combine this with POeQTL results from before using the sum of gene expression, especially for genes which we don’t have maternal or paternal expression.

99 |


Ym ∼ XSNP + PO + PO ⋅ XSNP

100 |


Yp ∼ XSNP + PO + PO ⋅ XSNP

101 | 102 | 103 | 104 | 105 | 106 | 107 | 108 | 109 | 110 | 111 | 112 | 113 | 114 | 115 | 116 | 117 | 118 | 119 | 120 | 121 | 122 | 123 | 124 | 125 | 126 | 127 | 128 | 129 | 130 | 131 | 132 | 133 | 134 | 135 | 136 | 137 | 138 | 139 | 140 | 141 | 142 | 143 | 144 | 145 | 146 | 147 | 148 | 149 | 150 | 151 | 152 | 153 | 154 | 155 | 156 | 157 | 158 | 159 | 160 | 161 | 162 | 163 | 164 | 165 | 166 | 167 | 168 | 169 | 170 | 171 | 172 | 173 | 174 | 175 | 176 | 177 | 178 | 179 | 180 | 181 | 182 | 183 | 184 | 185 | 186 | 187 | 188 | 189 | 190 | 191 | 192 | 193 | 194 | 195 | 196 | 197 | 198 | 199 | 200 | 201 | 202 | 203 | 204 | 205 |
[tab:Significant Genes] Significant genes from sign test (p-values in column 3) with weighted Z score with corresponding p-values in column 4 and 5, respectively. Imprinted as defined by geneimprint.com database.
GeneImprintedGenepvalueweighted Zscoreweighted pvalue
ZDBF2yes7e-3745.570
NHP2L1no, Docherty et al. (Docherty et al. 2014)7e-3118.982e-80
L3MBTL1yes2e-2935.731e-279
PEG10yes2e-2951.340
SNHG14no, Baran et. al (Baran et al. 2015)8e-2741.090
ZNF331no, Baran et. al (Baran et al. 2015)3e-2330.282e-201
KCNQ1yes4e-21-28.944e-184
LPAR6no, Baran et. al (Baran et al. 2015)7e-2133.504e-246
FAM50Byes4e-2028.892e-183
PXDC1no, neighboring gene of FAM50B3e-1416.056e-58
PWAR6no, Prader Willi/Angelman Region 61e-0925.592e-144
NAP1L5yes3e-0721.053e-98
ATP6V0D1no1e-06-5.407e-8
206 |
207 |
208 |

Baran, Yael, Meena Subramaniam, Anne Biton, Taru Tukiainen, Emily K Tsang, Manuel A Rivas, Matti Pirinen, et al. 2015. “The landscape of genomic imprinting across diverse adult human tissues.” Genome Research 25 (7): 927–36.

209 |
210 |
211 |

Dobin, Alexander, Carrie A Davis, Felix Schlesinger, Jorg Drenkow, Chris Zaleski, Sonali Jha, Philippe Batut, Mark Chaisson, and Thomas R Gingeras. 2012. “STAR: ultrafast universal RNA-seq aligner.” Bioinformatics 29 (1): 15–21.

212 |
213 |
214 |

Docherty, Louise E, Faisal I Rezwan, Rebecca L Poole, Hannah Jagoe, Hannah Lake, Gabrielle A Lockett, Hasan Arshad, et al. 2014. “Genome-wide DNA methylation analysis of patients with imprinting disorders identifies differentially methylated regions associated with novel candidate imprinted genes.” Journal of Medical Genetics 51 (4): 229–38.

215 |
216 |
217 |

Geijn, Bryce van de, Graham McVicker, Yoav Gilad, and Jonathan K Pritchard. 2015. “WASP: allele-specific software for robust molecular quantitative trait locus discovery.” Nature Methods 12 (11): 1061–3.

218 |
219 |
220 |

Jun, Goo, Matthew Flickinger, Kurt N Hetrick, Jane M Romm, Kimberly F Doheny, Goncalo R Abecasis, Michael Boehnke, and Hyun Min Kang. 2012. “Detecting and Estimating Contamination of Human DNA Samples in Sequencing and Array-Based Genotype Data.” The American Journal of Human Genetics 91 (5): 839–48.

221 |
222 |
223 |

Mott, Richard, Wei Yuan, Pamela Kaisaki, Xiangchao Gan, James Cleak, Andrew Edwards, Amelie Baud, and Jonathan Flint. 2014. “The Architecture of Parent-of-Origin Effects in Mice.” Cell 156 (1-2): 332–42.

224 |
225 |
226 |

Mozaffari, S V, J M DeCara, S J Shah, R M Lang, Dan L Nicolae, and Carole Ober. 2017. “Parent of Origin Effects on Quantitative Phenotypes in a Founder Population.” bioRxiv.

227 |
228 |
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