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2023
Hale RC, Owen N, Yuan B, Chinn IK. Phenotypic Variability of SOCS1 Haploinsufficiency. J Clin Immunol. 2023 ;43(5):902-906.
Shao Y, Zhou L, Li F, Zhao L, Zhang B-L, Shao F, Chen J-W, Chen C-Y, Bi X, Zhuang X-L, Zhu H-L, Hu J, Sun Z, Li X, Wang D, Rivas-González I, Wang S, Wang Y-M, Chen W, Li G, Lu H-M, Liu Y, Kuderna LFK, Farh KKai-How, Fan P-F, Yu L, Li M, Liu Z-J, Tiley GP, Yoder AD, Roos C, Hayakawa T, Marques-Bonet T, Rogers J, Stenson PD, Cooper DN, Schierup MHeide, Yao Y-G, Zhang Y-P, Wang W, Qi X-G, Zhang G, Wu D-D. Phylogenomic analyses provide insights into primate evolution. Science. 2023 ;380(6648):913-924.
Petit F, Longoni M, Wells J, Maser RS, Bogenschutz EL, Dysart MJ, Contreras HTM, Frénois F, Pober BR, Clark RD, Giampietro PF, Ropers HH, Hu H, Loscertales M, Wagner R, Ai X, Brand H, Jourdain A-S, Delrue M-A, Gilbert-Dussardier B, Devisme L, Keren B, McCulley DJ, Qiao L, Hernan R, Wynn J, Scott TM, Calame DG, Coban-Akdemir Z, Hernandez P, Hernandez-Garcia A, Yonath H, Lupski JR, Shen Y, Chung WK, Scott DA, Bult CJ, Donahoe PK, High FA. PLS3 missense variants affecting the actin-binding domains cause X-linked congenital diaphragmatic hernia and body-wall defects. Am J Hum Genet. 2023 ;110(10):1787-1803.
Li X, Quick C, Zhou H, Gaynor SM, Liu Y, Chen H, Selvaraj MSunitha, Sun R, Dey R, Arnett DK, Bielak LF, Bis JC, Blangero J, Boerwinkle E, Bowden DW, Brody JA, Cade BE, Correa A, L Cupples A, Curran JE, de Vries PS, Duggirala R, Freedman BI, Göring HHH, Guo X, Haessler J, Kalyani RR, Kooperberg C, Kral BG, Lange LA, Manichaikul A, Martin LW, McGarvey ST, Mitchell BD, Montasser ME, Morrison AC, Naseri T, O'Connell JR, Palmer ND, Peyser PA, Psaty BM, Raffield LM, Redline S, Reiner AP, Reupena M'aSefuiva, Rice KM, Rich SS, Sitlani CM, Smith JA, Taylor KD, Vasan RS, Willer CJ, Wilson JG, Yanek LR, Zhao W, Rotter JI, Natarajan P, Peloso GM, Li Z, Lin X. Powerful, scalable and resource-efficient meta-analysis of rare variant associations in large whole genome sequencing studies. Nat Genet. 2023 ;55(1):154-164.
Ufomadu P, Fu S, Huynh D. Prevalence of Rhabdomyosarcoma in the U.S. from 2017-2018: A SEER study. J Natl Med Assoc. 2023 ;115(4):403-404.
Tin A, Sullivan KJ, Walker KA, Bressler J, Talluri R, Yu B, Simino J, Gudmundsdottir V, Emilsson V, Jennings LL, Launer L, Mei H, Boerwinkle E, B Windham G, Gottesman R, Gudnason V, Coresh J, Fornage M, Mosley TH. Proteomic Analysis Identifies Circulating Proteins Associated With Plasma Amyloid-β and Incident Dementia. Biol Psychiatry Glob Open Sci. 2023 ;3(3):490-499.
Walker KA, Chen J, Shi L, Yang Y, Fornage M, Zhou L, Schlosser P, Surapaneni A, Grams ME, Duggan MR, Peng Z, Gomez GT, Tin A, Hoogeveen RC, Sullivan KJ, Ganz P, Lindbohm JV, Kivimaki M, Nevado-Holgado AJ, Buckley N, Gottesman RF, Mosley TH, Boerwinkle E, Ballantyne CM, Coresh J. Proteomics analysis of plasma from middle-aged adults identifies protein markers of dementia risk in later life. Sci Transl Med. 2023 ;15(705):eadf5681.
Holmstrom L, Chaudhary NS, Nakamura K, Chugh H, Uy-Evanado A, Norby F, Metcalf GA, Menon VK, Yu B, Boerwinkle E, Chugh SS, Akdemir Z, Kransdorf EP. Rare Genetic Variants Associated With Sudden Cardiac Arrest in the Young: A Prospective, Population-Based Study. Circ Genom Precis Med. 2023 ;16(4):404-405.
Fiziev P, McRae J, Ulirsch JC, Dron JS, Hamp T, Yang Y, Wainschtein P, Ni Z, Schraiber JG, Gao H, Cable D, Field Y, Aguet F, Fasnacht M, Metwally A, Rogers J, Marques-Bonet T, Rehm HL, O'Donnell-Luria A, Khera AV, Farh KKai-How. Rare penetrant mutations confer severe risk of common diseases. medRxiv. 2023 ;.
Fiziev PP, McRae J, Ulirsch JC, Dron JS, Hamp T, Yang Y, Wainschtein P, Ni Z, Schraiber JG, Gao H, Cable D, Field Y, Aguet F, Fasnacht M, Metwally A, Rogers J, Marques-Bonet T, Rehm HL, O'Donnell-Luria A, Khera AV, Farh KKai-How. Rare penetrant mutations confer severe risk of common diseases. Science. 2023 ;380(6648):eabo1131.
Jolly A, Du H, Borel C, Chen N, Zhao S, Grochowski CM, Duan R, Fatih JM, Dawood M, Salvi S, Jhangiani SN, Muzny DM, Koch A, Rouskas K, Glentis S, Deligeoroglou E, Bacopoulou F, Wise CA, Dietrich JE, Van den Veyver IB, Dimas AS, Brucker S, V Sutton R, Gibbs RA, Antonarakis SE, Wu N, Coban-Akdemir ZH, Zhu L, Posey JE, Lupski JR. Rare variant enrichment analysis supports as a contributory driver gene in the etiology of Mayer-Rokitansky-Küster-Hauser syndrome. HGG Adv. 2023 ;4(3):100188.
Wang Y, Selvaraj MSunitha, Li X, Li Z, Holdcraft JA, Arnett DK, Bis JC, Blangero J, Boerwinkle E, Bowden DW, Cade BE, Carlson JC, Carson AP, Chen Y-DIda, Curran JE, de Vries PS, Dutcher SK, Ellinor PT, Floyd JS, Fornage M, Freedman BI, Gabriel S, Germer S, Gibbs RA, Guo X, He J, Heard-Costa N, Hildalgo B, Hou L, Irvin MR, Joehanes R, Kaplan RC, Kardia SLr, Kelly TN, Kim R, Kooperberg C, Kral BG, Levy D, Li C, Liu C, Lloyd-Jone D, Loos RJf, Mahaney MC, Martin LW, Mathias RA, Minster RL, Mitchell BD, Montasser ME, Morrison AC, Murabito JM, Naseri T, O'Connell JR, Palmer ND, Preuss MH, Psaty BM, Raffield LM, Rao DC, Redline S, Reiner AP, Rich SS, Ruepena M'aSefuiva, Sheu WH-H, Smith JA, Smith A, Tiwari HK, Tsai MY, Viaud-Martinez KA, Wang Z, Yanek LR, Zhao W, Rotter JI, Lin X, Natarajan P, Peloso GM. Rare variants in long non-coding RNAs are associated with blood lipid levels in the TOPMed Whole Genome Sequencing Study. medRxiv. 2023 ;.
Wang Y, Selvaraj MSunitha, Li X, Li Z, Holdcraft JA, Arnett DK, Bis JC, Blangero J, Boerwinkle E, Bowden DW, Cade BE, Carlson JC, Carson AP, Chen Y-DIda, Curran JE, de Vries PS, Dutcher SK, Ellinor PT, Floyd JS, Fornage M, Freedman BI, Gabriel S, Germer S, Gibbs RA, Guo X, He J, Heard-Costa N, Hildalgo B, Hou L, Irvin MR, Joehanes R, Kaplan RC, Kardia SLr, Kelly TN, Kim R, Kooperberg C, Kral BG, Levy D, Li C, Liu C, Lloyd-Jone D, Loos RJf, Mahaney MC, Martin LW, Mathias RA, Minster RL, Mitchell BD, Montasser ME, Morrison AC, Murabito JM, Naseri T, O'Connell JR, Palmer ND, Preuss MH, Psaty BM, Raffield LM, Rao DC, Redline S, Reiner AP, Rich SS, Ruepena M'aSefuiva, Sheu WH-H, Smith JA, Smith A, Tiwari HK, Tsai MY, Viaud-Martinez KA, Wang Z, Yanek LR, Zhao W, Rotter JI, Lin X, Natarajan P, Peloso GM. Rare variants in long non-coding RNAs are associated with blood lipid levels in the TOPMed whole-genome sequencing study. Am J Hum Genet. 2023 ;110(10):1704-1717.
Bi W, Yuan B, Liu P, Murry JB, Qin X, Xia F, Quach T, Cooper LM, Wiszniewska J, Hixson P, Peacock S, Tonk VS, Huff RW, Ortega V, Lupski JR, Scherer SE, Littlejohn ROkashah, Velagaleti GVN, Roeder ER, Cheung SWai. Recurring germline mosaicism in a family due to reversion of an inherited derivative chromosome 8 from an 8;21 translocation with interstitial telomeric sequences. J Med Genet. 2023 ;60(6):547-556.
Qian X, Srinivasan T, He J, Chen R. The Role of Ceramide in Inherited Retinal Disease Pathology. Adv Exp Med Biol. 2023 ;1415:303-307.
Kolmogorov M, Billingsley KJ, Mastoras M, Meredith M, Monlong J, Lorig-Roach R, Asri M, Jerez PAlvarez, Malik L, Dewan R, Reed X, Genner RM, Daida K, Behera S, Shafin K, Pesout T, Prabakaran J, Carnevali P, Yang J, Rhie A, Scholz SW, Traynor BJ, Miga KH, Jain M, Timp W, Phillippy AM, Chaisson M, Sedlazeck FJ, Blauwendraat C, Paten B. Scalable Nanopore sequencing of human genomes provides a comprehensive view of haplotype-resolved variation and methylation. bioRxiv. 2023 ;.
Kolmogorov M, Billingsley KJ, Mastoras M, Meredith M, Monlong J, Lorig-Roach R, Asri M, Jerez PAlvarez, Malik L, Dewan R, Reed X, Genner RM, Daida K, Behera S, Shafin K, Pesout T, Prabakaran J, Carnevali P, Yang J, Rhie A, Scholz SW, Traynor BJ, Miga KH, Jain M, Timp W, Phillippy AM, Chaisson M, Sedlazeck FJ, Blauwendraat C, Paten B. Scalable Nanopore sequencing of human genomes provides a comprehensive view of haplotype-resolved variation and methylation. Nat Methods. 2023 ;20(10):1483-1492.
Raja KKumar Boll, Yeung K, Shim Y-K, Li Y, Chen R, Mardon G. A single cell genomics atlas of the Drosophila larval eye reveals distinct photoreceptor developmental timelines. Nat Commun. 2023 ;14(1):7205.
Wang J, Cheng X, Liang Q, Owen LA, Lu J, Zheng Y, Wang M, Chen S, DeAngelis MM, Li Y, Chen R. Single-cell multiomics of the human retina reveals hierarchical transcription factor collaboration in mediating cell type-specific effects of genetic variants on gene regulation. Genome Biol. 2023 ;24(1):269.
Harris RA, McAllister JM, Strauss JF. Single-Cell RNA-Seq Identifies Pathways and Genes Contributing to the Hyperandrogenemia Associated with Polycystic Ovary Syndrome. Int J Mol Sci. 2023 ;24(13).
Kalef-Ezra E, Turan ZGozde, Perez-Rodriguez D, Bomann I, Behera S, Morley C, Scholz SW, Jaunmuktane Z, Demeulemeester J, Sedlazeck FJ, Proukakis C. Single-cell somatic copy number variants in brain using different amplification methods and reference genomes. bioRxiv. 2023 ;.
Dou J, Tan Y, Kock KHong, Wang J, Cheng X, Tan LMin, Han KYeon, Hon C-C, Park W-Y, Shin JW, Jin H, Wang Y, Chen H, Ding L, Prabhakar S, Navin N, Chen R, Chen K. Single-nucleotide variant calling in single-cell sequencing data with Monopogen. Nat Biotechnol. 2023 ;.
Bogaert E, Garde A, Gautier T, Rooney K, Duffourd Y, LeBlanc P, van Reempts E, Mau-Them FTran, Wentzensen IM, Au KSing, Richardson K, Northrup H, Gatinois V, Geneviève D, Louie RJ, Lyons MJ, Laulund LWalentin, Brasch-Andersen C, Juul TMaxel, It FEl, Marle N, Callier P, Relator R, Haghshenas S, McConkey H, Kerkhof J, Cesario C, Novelli A, Brunetti-Pierri N, Pinelli M, Pennamen P, Naudion S, Legendre M, Courdier C, Trimouille A, Fenzy MDoco, Pais L, Yeung A, Nugent K, Roeder ER, Mitani T, Posey JE, Calame D, Yonath H, Rosenfeld JA, Musante L, Faletra F, Montanari F, Sartor G, Vancini A, Seri M, Besmond C, Poirier K, Hubert L, Hemelsoet D, Munnich A, Lupski JR, Philippe C, Thauvin-Robinet C, Faivre L, Sadikovic B, Govin J, Dermaut B, Vitobello A. SRSF1 haploinsufficiency is responsible for a syndromic developmental disorder associated with intellectual disability. Am J Hum Genet. 2023 ;110(5):790-808.
Li X, Chen H, Selvaraj MSunitha, Van Buren E, Zhou H, Wang Y, Sun R, McCaw ZR, Yu Z, Arnett DK, Bis JC, Blangero J, Boerwinkle E, Bowden DW, Brody JA, Cade BE, Carson AP, Carlson JC, Chami N, Chen Y-DIda, Curran JE, de Vries PS, Fornage M, Franceschini N, Freedman BI, Gu C, Heard-Costa NL, He J, Hou L, Hung Y-J, Irvin MR, Kaplan RC, Kardia SLR, Kelly T, Konigsberg I, Kooperberg C, Kral BG, Li C, Loos RJF, Mahaney MC, Martin LW, Mathias RA, Minster RL, Mitchell BD, Montasser ME, Morrison AC, Palmer ND, Peyser PA, Psaty BM, Raffield LM, Redline S, Reiner AP, Rich SS, Sitlani CM, Smith JA, Taylor KD, Tiwari H, Vasan RS, Wang Z, Yanek LR, Yu B, Rice KM, Rotter JI, Peloso GM, Natarajan P, Li Z, Liu Z, Lin X. A statistical framework for powerful multi-trait rare variant analysis in large-scale whole-genome sequencing studies. bioRxiv. 2023 ;.
Wang N, Yu B, Jun G, Qi Q, Durazo-Arvizu RA, Lindström S, Morrison AC, Kaplan RC, Boerwinkle E, Chen H. StocSum: stochastic summary statistics for whole genome sequencing studies. bioRxiv. 2023 ;.