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Monkol received an undergraduate degree in Engineering (Computer Engineering) in 2000 at the University of New South Wales (UNSW) and then worked for IBM for 3.5 years. He returned to UNSW and completed undergraduate degrees in Science (Physiology) and Engineering (Bioinformatics) and received the University Medal in 2007. He completed his PhD (Medicine) at the University of Sydney in 2012 with the thesis topic: Functional differences between alpha-actinin-2 and alpha-actinin-3. Monkol did his post-doctoral training in Daniel MacArthur’s lab based at Massachusetts General Hospital, Harvard Medical School and the Broad Institute.

He was the lead author/analyst for the Exome Aggregation Consortium (ExAC) project that was published in Nature 2016. He went on to lead the NIH funded Broad Center for Mendelian Genomics (CMG) analysis team. As lead analyst, he oversaw the analysis strategy for all major CMG collaborations and organized monthly meetings to foster sharing of new methods and analysis amongst the rare disease community. He also coordinated the data processing and preliminary analysis of NIH Gabriella Miller Kids First (GMKF) cohorts sequenced or reprocessed at the Broad Institute.

Monkol has a strong passion for rare muscle disease research as a patient with Limb Girdle Muscular dystrophy (LGMD2G). During his time in the Broad Institute, he lead the exome/genome analysis of MYOSEQ (European cohort of >1000 LGMD patients) and SeqNMD (an international consortium of undiagnosed rare muscle diseases) which has resulted in novel disease gene discovery.

\",\"photo\":{\"hiResUrl\":\"https://files-profile.medicine.yale.edu/images/39fc4db7-5287-4083-ab63-be2111f00b46\",\"url\":\"https://ysm-res.cloudinary.com/image/upload/v1/yms/prod/39fc4db7-5287-4083-ab63-be2111f00b46\",\"altText\":\"Monkol Lek\",\"width\":2508,\"height\":3344,\"imageVariants\":[{\"dimension\":\"Square\",\"url\":\"https://ysm-res.cloudinary.com/image/upload/v1/yms/prod/bdbd2e01-9af8-4809-a12a-7bb6f446cc9a\",\"width\":2282,\"height\":2282},{\"dimension\":\"Rectangle\",\"url\":\"https://ysm-res.cloudinary.com/image/upload/v1/yms/prod/bee65be0-fdd6-4ffd-90e6-f255b964ff14\",\"width\":2282,\"height\":2853}]},\"gallery\":null,\"organizations\":[{\"id\":118611,\"name\":\"Center for Biomedical Data Science\",\"url\":\"https://medicine.yale.edu/cbds/\"},{\"id\":109533,\"name\":\"Computational Biology and Bioinformatics\",\"url\":\"http://bbs.yale.edu/computational\"},{\"id\":108854,\"name\":\"Genetics\",\"url\":\"https://medicine.yale.edu/genetics\"},{\"id\":109539,\"name\":\"Molecular Cell Biology, Genetics and Development\",\"url\":\"http://bbs.yale.edu/molecularcell\"},{\"id\":109532,\"name\":\"Yale Combined Program in the Biological and Biomedical Sciences (BBS)\",\"url\":\"http://bbs.yale.edu\"},{\"id\":110762,\"name\":\"Yale University\",\"url\":\"https://www.yale.edu/\"}],\"appointmentOrganizations\":[{\"id\":108854,\"name\":\"Genetics\",\"url\":\"https://medicine.yale.edu/genetics\"}],\"educations\":[{\"degree\":\"PhD\",\"institution\":\"University of Sydney, Medicine (2012)\"},{\"degree\":\"BSc\",\"institution\":\"University of New South Wales, Physiology (2007)\"},{\"degree\":\"BE\",\"institution\":\"University of New South Wales, Bioinformatics (2007)\"},{\"degree\":\"BE\",\"institution\":\"University of New South Wales, Computer Engineering (2001)\"},{\"degree\":\"Senior Research Fellow\",\"institution\":\"Broad Institute of MIT and Harvard\"},{\"degree\":\"Post-doctoral Fellow\",\"institution\":\"Harvard Medical School\"}],\"honors\":[{\"award\":\"Development Grant\",\"awardingOrganization\":\"Muscular Dystrophy Association\",\"date\":\"2016\"},{\"award\":\"CJ Martin Fellowship\",\"awardingOrganization\":\"Australian National Health and Medical Research Council (NHMRC)\",\"date\":\"2013\"},{\"award\":\"Sir Keith Murdoch Fellowship\",\"awardingOrganization\":\"Australian American Association\",\"date\":\"2012\"},{\"award\":\"Australian Post-graduate Award\",\"awardingOrganization\":\"University of Sydney\",\"date\":\"2009\"},{\"award\":\"University Medal\",\"awardingOrganization\":\"University of New South Wales\",\"date\":\"2008\"}],\"services\":[],\"activities\":[]},\"researchTab\":{\"research\":{\"description\":null,\"summary\":\"

The lab is focused on understanding the genetic mechanism of rare diseases that may lead to rational approaches for therapies. Initially we are aimed at improving the diagnosis of rare neuromuscular diseases through the following approaches:

Methods Development

In recent years, large genomic data sets such as ExAC have been made publicly available and are a powerful resource for methods development. Our goal is to use these resources to build computational methods to improve our interpretation and prioritization of near-coding variants that are captured by exome sequencing but are often filtered or not considered due to difficulties in their interpretation. Further understanding of these classes of variants may contribute to improving the diagnosis rate in rare diseases.

Novel disease gene discovery

In collaboration with the Center of Mendelian Genomics, we aim to build and sequence a large cohort of undiagnosed neuromuscular disease patients to identify novel genes from exome and genome sequencing. These cohorts will be mainly non-European with a particular focus on patients from East Asia and South Asia. As part of these projects, we aim to develop and share tools and methods specific to rare disease analysis.

Detection of non-coding variants associated with disease

We aim to develop a cohort of recessive disease patients with only one pathogenic variant identified and based on several lines of evidence are likely to harbor another pathogenic mutation. Genome sequencing of these patients is likely to reveal non-coding, structural variants or novel mechanisms that were undetected by exome sequencing.

As a complementary approach, we will use saturating mutagenesis (i.e. tiling of sgRNA) to systematically disrupt regions in the vicinity of disease genes to identify non-coding regions that may impact gene function.

Interpretation of variants of unknown significance

A large challenge of rare disease diagnosis is the interpretation or correcting misinterpretations of rare missense variants in well established disease genes. Computational and analytical approaches take several lines of evidence in to consideration such as allele frequency and conservation but rarely physiologically relevant functional assays. Using cells from patients and healthy controls, we will design scalable high-throughput assays that can distinguish pathogenic from benign variants in muscle disease.

The methods and models to better understand the genetic underpinnings of rare disease can then be used to design and test therapies for neuromuscular disease patients.

\",\"researchInterests\":[\"Genetics\",\"Genetics, Medical\",\"Neuromuscular Diseases\",\"Genomics\"],\"healthInterests\":[],\"researchImagesGallery\":null},\"publications\":[{\"title\":\"Analysis of protein-coding genetic variation in 60,706 humans.\",\"citation\":\"Lek M, Karczewski KJ, Minikel EV, Samocha KE, Banks E, Fennell T, O'Donnell-Luria AH, Ware JS, Hill AJ, Cummings BB, Tukiainen T, Birnbaum DP, Kosmicki JA, Duncan LE, Estrada K, Zhao F, Zou J, Pierce-Hoffman E, Berghout J, Cooper DN, Deflaux N, DePristo M, Do R, Flannick J, Fromer M, Gauthier L, Goldstein J, Gupta N, Howrigan D, Kiezun A, Kurki MI, Moonshine AL, Natarajan P, Orozco L, Peloso GM, Poplin R, Rivas MA, Ruano-Rubio V, Rose SA, Ruderfer DM, Shakir K, Stenson PD, Stevens C, Thomas BP, Tiao G, Tusie-Luna MT, Weisburd B, Won HH, Yu D, Altshuler DM, Ardissino D, Boehnke M, Danesh J, Donnelly S, Elosua R, Florez JC, Gabriel SB, Getz G, Glatt SJ, Hultman CM, Kathiresan S, Laakso M, McCarroll S, McCarthy MI, McGovern D, McPherson R, Neale BM, Palotie A, Purcell SM, Saleheen D, Scharf JM, Sklar P, Sullivan PF, Tuomilehto J, Tsuang MT, Watkins HC, Wilson JG, Daly MJ, MacArthur DG. Analysis of protein-coding genetic variation in 60,706 humans. Nature 2016, 536:285-91.\",\"year\":2016,\"link\":{\"url\":\"https://www.ncbi.nlm.nih.gov/pubmed/27535533\",\"text\":\"Analysis of protein-coding genetic variation in 60,706 humans.\"}},{\"title\":\"Patterns of genic intolerance of rare copy number variation in 59,898 human exomes.\",\"citation\":\"Ruderfer DM, Hamamsy T, Lek M, Karczewski KJ, Kavanagh D, Samocha KE, Daly MJ, MacArthur DG, Fromer M, Purcell SM. Patterns of genic intolerance of rare copy number variation in 59,898 human exomes. Nature Genetics 2016, 48:1107-11.\",\"year\":2016,\"link\":{\"url\":\"https://www.ncbi.nlm.nih.gov/pubmed/27533299\",\"text\":\"Patterns of genic intolerance of rare copy number variation in 59,898 human exomes.\"}},{\"title\":\"Quantifying prion disease penetrance using large population control cohorts.\",\"citation\":\"Minikel EV, Vallabh SM, Lek M, Estrada K, Samocha KE, Sathirapongsasuti JF, McLean CY, Tung JY, Yu LP, Gambetti P, Blevins J, Zhang S, Cohen Y, Chen W, Yamada M, Hamaguchi T, Sanjo N, Mizusawa H, Nakamura Y, Kitamoto T, Collins SJ, Boyd A, Will RG, Knight R, Ponto C, Zerr I, Kraus TF, Eigenbrod S, Giese A, Calero M, de Pedro-Cuesta J, Haïk S, Laplanche JL, Bouaziz-Amar E, Brandel JP, Capellari S, Parchi P, Poleggi A, Ladogana A, O'Donnell-Luria AH, Karczewski KJ, Marshall JL, Boehnke M, Laakso M, Mohlke KL, Kähler A, Chambert K, McCarroll S, Sullivan PF, Hultman CM, Purcell SM, Sklar P, van der Lee SJ, Rozemuller A, Jansen C, Hofman A, Kraaij R, van Rooij JG, Ikram MA, Uitterlinden AG, van Duijn CM, Daly MJ, MacArthur DG. Quantifying prion disease penetrance using large population control cohorts. Science Translational Medicine 2016, 8:322ra9.\",\"year\":2016,\"link\":{\"url\":\"https://www.ncbi.nlm.nih.gov/pubmed/26791950\",\"text\":\"Quantifying prion disease penetrance using large population control cohorts.\"}},{\"title\":\"Human genomics. Effect of predicted protein-truncating genetic variants on the human transcriptome.\",\"citation\":\"Rivas MA, Pirinen M, Conrad DF, Lek M, Tsang EK, Karczewski KJ, Maller JB, Kukurba KR, DeLuca DS, Fromer M, Ferreira PG, Smith KS, Zhang R, Zhao F, Banks E, Poplin R, Ruderfer DM, Purcell SM, Tukiainen T, Minikel EV, Stenson PD, Cooper DN, Huang KH, Sullivan TJ, Nedzel J, Bustamante CD, Li JB, Daly MJ, Guigo R, Donnelly P, Ardlie K, Sammeth M, Dermitzakis ET, McCarthy MI, Montgomery SB, Lappalainen T, MacArthur DG. Human genomics. Effect of predicted protein-truncating genetic variants on the human transcriptome. Science (New York, N.Y.) 2015, 348:666-9.\",\"year\":2015,\"link\":{\"url\":\"https://www.ncbi.nlm.nih.gov/pubmed/25954003\",\"text\":\"Human genomics. Effect of predicted protein-truncating genetic variants on the human transcriptome.\"}},{\"title\":\"Improving genetic diagnosis in Mendelian disease with transcriptome sequencing.\",\"citation\":\"Cummings BB, Marshall JL, Tukiainen T, Lek M, Donkervoort S, Foley AR, Bolduc V, Waddell LB, Sandaradura SA, O'Grady GL, Estrella E, Reddy HM, Zhao F, Weisburd B, Karczewski KJ, O'Donnell-Luria AH, Birnbaum D, Sarkozy A, Hu Y, Gonorazky H, Claeys K, Joshi H, Bournazos A, Oates EC, Ghaoui R, Davis MR, Laing NG, Topf A, Kang PB, Beggs AH, North KN, Straub V, Dowling JJ, Muntoni F, Clarke NF, Cooper ST, Bönnemann CG, MacArthur DG. Improving genetic diagnosis in Mendelian disease with transcriptome sequencing. Science Translational Medicine 2017, 9.\",\"year\":2017,\"link\":{\"url\":\"https://www.ncbi.nlm.nih.gov/pubmed/28424332\",\"text\":\"Improving genetic diagnosis in Mendelian disease with transcriptome sequencing.\"}},{\"title\":\"Use of Whole-Exome Sequencing for Diagnosis of Limb-Girdle Muscular Dystrophy: Outcomes and Lessons Learned.\",\"citation\":\"Ghaoui R, Cooper ST, Lek M, Jones K, Corbett A, Reddel SW, Needham M, Liang C, Waddell LB, Nicholson G, O'Grady G, Kaur S, Ong R, Davis M, Sue CM, Laing NG, North KN, MacArthur DG, Clarke NF. Use of Whole-Exome Sequencing for Diagnosis of Limb-Girdle Muscular Dystrophy: Outcomes and Lessons Learned. JAMA Neurology 2015, 72:1424-32.\",\"year\":2015,\"link\":{\"url\":\"https://www.ncbi.nlm.nih.gov/pubmed/26436962\",\"text\":\"Use of Whole-Exome Sequencing for Diagnosis of Limb-Girdle Muscular Dystrophy: Outcomes and Lessons Learned.\"}},{\"title\":\"Diagnosis and etiology of congenital muscular dystrophy: We are halfway there.\",\"citation\":\"O'Grady GL, Lek M, Lamande SR, Waddell L, Oates EC, Punetha J, Ghaoui R, Sandaradura SA, Best H, Kaur S, Davis M, Laing NG, Muntoni F, Hoffman E, MacArthur DG, Clarke NF, Cooper S, North K. Diagnosis and etiology of congenital muscular dystrophy: We are halfway there. Annals Of Neurology 2016, 80:101-11.\",\"year\":2016,\"link\":{\"url\":\"https://www.ncbi.nlm.nih.gov/pubmed/27159402\",\"text\":\"Diagnosis and etiology of congenital muscular dystrophy: We are halfway there.\"}},{\"title\":\"The Challenge of Next Generation Sequencing in the Context of Neuromuscular Diseases.\",\"citation\":\"Lek M, MacArthur D. 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Trends In Genetics : TIG 2012, 28:303-5.\",\"year\":2012,\"link\":{\"url\":\"https://www.ncbi.nlm.nih.gov/pubmed/22658726\",\"text\":\"The uncertain road towards genomic medicine.\"}}],\"clinicalTrials\":[{\"url\":\"/ycci/trial/581/\",\"title\":\"Pediatric Genomics Discovery Program (PGDP)\",\"conditions\":[\"Children's Health\",\"Genetics - Pediatric\"]}],\"coauthors\":[]},\"patientCareTab\":null,\"newsTab\":{\"searchUrl\":null,\"news\":[{\"id\":\"22134\",\"bylineDate\":\"2019-12-17T21:28:16-05:00\",\"title\":\"Rare Diseases: Customizing Cures, Patient by Patient\",\"summary\":\"Yale geneticist with muscular dystrophy wants to cure a rare form of the disease.\",\"thumbnail\":{\"url\":\"https://ysm-res.cloudinary.com/image/upload/v1/yms/prod/651ad272-ff8a-4704-b98c-a4d2b3c7bece\",\"altText\":null,\"width\":1242,\"height\":699,\"imageVariants\":[{\"dimension\":\"Square\",\"url\":\"https://ysm-res.cloudinary.com/image/upload/v1/yms/prod/c5b235a8-57c2-4bac-b4e0-b9d2a6004b85\",\"width\":633,\"height\":633},{\"dimension\":\"Rectangle\",\"url\":\"https://ysm-res.cloudinary.com/image/upload/v1/yms/prod/67672318-1452-488e-921e-c4305d7607e6\",\"width\":1241,\"height\":666}]},\"url\":\"https://www.yalemedicine.org/stories/rare-diseases/\",\"isFeatured\":false,\"source\":\"Yale Medicine\"},{\"id\":\"21953\",\"bylineDate\":\"2019-11-26T05:00:00-05:00\",\"title\":\"The Inaugural Walter J. 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That’s because Lek has a rare disease, a form of muscular dystrophy that requires him to use a wheelchair at times. His real-life experience has led him to eschew pure research in favor of finding practical treatments.\",\"thumbnail\":{\"url\":\"https://ysm-res.cloudinary.com/image/upload/v1/yms/prod/1371ffde-d497-416a-b8f1-4daf03abdeca\",\"altText\":null,\"width\":720,\"height\":960,\"imageVariants\":[{\"dimension\":\"Square\",\"url\":\"https://ysm-res.cloudinary.com/image/upload/v1/yms/prod/4ba70f5b-e532-4084-9e5d-b9b1213b974b\",\"width\":494,\"height\":494},{\"dimension\":\"Rectangle\",\"url\":\"https://ysm-res.cloudinary.com/image/upload/v1/yms/prod/0566ec51-0731-4fe5-93fb-e81f5200bbe3\",\"width\":720,\"height\":494}]},\"url\":\"https://medicine.yale.edu/news/yale-medicine-magazine/yale-school-of-medicine-rare-disease-researcher-is.aspx\",\"isFeatured\":false,\"source\":\"Yale Medicine Magazine\"}]},\"locationsTab\":{\"addresses\":[{\"id\":23689,\"address\":{\"id\":345,\"officeName\":\"S341C\",\"name\":\"The Anlyan Center\",\"addressLine1\":\"300 Cedar Street\",\"addressLine2\":\"\",\"city\":\"New Haven\",\"region\":\"CT\",\"country\":\"United States\",\"postalCode\":\"06519\"},\"geoPoint\":{\"latitude\":41.3014196,\"longitude\":-72.9338371},\"phones\":[],\"activeHours\":null,\"website\":null},{\"id\":23690,\"address\":{\"id\":345,\"officeName\":\"S320\",\"name\":\"The Anlyan Center\",\"addressLine1\":\"300 Cedar Street\",\"addressLine2\":\"\",\"city\":\"New Haven\",\"region\":\"CT\",\"country\":\"United States\",\"postalCode\":\"06519\"},\"geoPoint\":{\"latitude\":41.3014196,\"longitude\":-72.9338371},\"phones\":[],\"activeHours\":null,\"website\":null}]},\"metaData\":{\"title\":\"Monkol Lek, PhD\",\"description\":\"Monkol received an undergraduate degree in Engineering (Computer Engineering) in 2000 at the University of New South Wales (UNSW) and then worked for IBM for 3.5 years. 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