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publications [2015/06/19 15:27]
ivan
publications [2017/05/05 12:30]
ivan [All Other Publications Since 2012]
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 ===== Selected Recent Publications ===== ===== Selected Recent Publications =====
  
-  ​- Francioli LC, Polak PP, Koren A, Menelaou A, Chun S, Renkens I; Genome of the Netherlands Consortium, van Duijn CM, Swertz M, Wijmenga C, van Ommen G, Slagboom PE, Boomsma DI, Ye K, Guryev V, Arndt PF, Kloosterman WP, de Bakker PI, **Sunyaev SR**. Genome-wide patterns and properties of de novo mutations in humans.\\ Nat Genet. (2015) ​[Epub ahead of print]. PubMed [[http://​www.ncbi.nlm.nih.gov/​pubmed/​25985141|PMID:​25985141]]. + 
-  - Do R, Balick D, Li H, Adzhubei I, **Sunyaev S**, Reich D. No evidence that selection has been less effective at removing deleterious mutations in Europeans than in Africans.\\ Nat Genet. 47(2):​126-31 (2015). PubMed [[http://​www.ncbi.nlm.nih.gov/​pubmed/​25581429|PMID:​25581429]]. +  - Cassa CA, Weghorn D, Balick DJ, Jordan DM, Nusinow D, Samocha KE, O'​Donnell-Luria A, MacArthur DG, Daly MJ, Beier DR, Sunyaev SR. Estimating the selective effects of heterozygous protein-truncating variants from human exome data. \\ Nat Genet. 2017 Apr 03 doi:​10.1038/​ng.3831. PubMed [[http://​www.ncbi.nlm.nih.gov/​pubmed/​28369035|PMID:​28369035]]. 
-  - Polak P, Karlić R, Koren A, Thurman R, Sandstrom R, Lawrence MS, Reynolds A, Rynes E, Vlahoviček K, Stamatoyannopoulos JA, **Sunyaev SR**. Cell-of-origin chromatin organization shapes the mutational landscape of cancer.\\ Nature 518(7539):​360-4 (2015). PubMed [[http://​www.ncbi.nlm.nih.gov/​pubmed/​25693567|PMID:​25693567]]. +  - Chun S, Casparino A, Patsopoulos NA, Croteau-Chonka DC, Raby BA, De Jager PL, Sunyaev SR, Cotsapas C. Limited statistical evidence for shared genetic effects of eQTLs and autoimmune disease-associated loci in three major immune cell types. \\ Nat Genet. 2017 Feb 20. doi: 10.1038/​ng.3795. PubMed [[http://​www.ncbi.nlm.nih.gov/​pubmed/​28218759|PMID:​28218759]]. 
-  - Zuk O, Schaffner SF, Samocha K, Do R, Hechter E, Kathiresan S, Daly MJ, Neale BM, **Sunyaev SR**, Lander ES.\\ Proc Natl Acad Sci. 111(4):​E455-64 (2014). PubMed [[http://​www.ncbi.nlm.nih.gov/​pubmed/​24443550|PMID:​24443550]]. +  - Sul JH, Cade BE, Cho MH, Qiao D, Silverman EK, Redline S, Sunyaev S. Increasing Generality and Power of Rare-Variant Tests by Utilizing Extended Pedigrees. \\ Am J Hum Genet. 2016 Oct 6;​99(4):​846-859. doi: 10.1016/​j.ajhg.2016.08.015. PubMed [[http://​www.ncbi.nlm.nih.gov/​pubmed/​27666371|PMID:​27666371]]. 
-  - Polak P, Lawrence MS, Haugen E, Stoletzki N, Stojanov P, Thurman RE, Garraway LA, Mirkin S, Getz G, Stamatoyannopoulos JA, **Sunyaev SR**. Reduced local mutation density in regulatory DNA of cancer genomes is linked to DNA repair.\\ Nat Biotechnol. 32(1):71-5 (2014). PubMed [[http://​www.ncbi.nlm.nih.gov/​pubmed/​24336318|PMID:​24336318]]. +  - Savova V, Chun S, Sohail M, McCole RB, Witwicki R, Gai L, Lenz TL, Wu CT, Sunyaev SR, Gimelbrant AA. Genes with monoallelic expression contribute disproportionately to genetic diversity in humans. \\ Nat Genet. 2016 Mar;​48(3):​231-7. doi: 10.1038/​ng.3493. PubMed [[http://​www.ncbi.nlm.nih.gov/​pubmed/​26808112|PMID:​26808112]].  
-  - Goldstein DB, Allen A, Keebler J, Margulies EH, Petrou S, Petrovski S, **Sunyaev S**. Sequencing studies in human genetics: design and interpretation.\\ Nat Rev Genet 14(7):​460-70 (2013). PubMed [[http://​www.ncbi.nlm.nih.gov/​pubmed/​23752795|PMID:​23752795]]. +  - Kazanov MD, Roberts SA, Polak P, Stamatoyannopoulos J, Klimczak LJ, Gordenin DA, Sunyaev SR. APOBEC-Induced Cancer Mutations Are Uniquely Enriched in Early-Replicating,​ Gene-Dense, and Active Chromatin Regions. \\ Cell Rep. 2015 Nov 10;​13(6):​1103-9. doi: 10.1016/​j.celrep.2015.09.077. Epub 2015 Oct 29. PubMed [[http://​www.ncbi.nlm.nih.gov/​pubmed/​26527001|PMID:​26527001]]. 
-  - Coste B, Houge G, Murray MF, Stitziel N, Bandell M, Giovanni MA, Philippakis A, Hoischen A, Riemer G, Steen U, Steen VM, Mathur J, Cox J, Lebo M, Rehm H, Weiss ST, Wood JN, Maas RL, **Sunyaev SR**, Patapoutian A. Gain-of-function mutations in the mechanically activated ion channel PIEZO2 cause a subtype of Distal Arthrogryposis.\\ Proc Natl Acad Sci U S A 110(12):​4667-72 (2013). PubMed [[http://​www.ncbi.nlm.nih.gov/​pubmed/​23487782|PMID:​23487782]]. +  - Akle S, Chun S, Jordan DM, Cassa CA. Mitigating false-positive associations in rare disease gene discovery.\\ Hum Mutat. 2015 Oct;​36(10):​998-1003. doi: 10.1002/​humu.22847. PubMed [[http://​www.ncbi.nlm.nih.gov/​pubmed/​26378430|PMID:​26378430]]. 
-  - Kiezun A, Pulit SL, Francioli LC, van Dijk F, Swertz M, Boomsma DI, van Duijn CM, Slagboom PE, van Ommen GJ, Wijmenga C; Genome of the Netherlands Consortium, de Bakker PI, **Sunyaev SR**. Deleterious alleles in the human genome are on average younger than neutral alleles of the same frequency.\\ PLoS Genet 9(2):​e1003301 (2013). PubMed [[http://​www.ncbi.nlm.nih.gov/​pubmed/​3468643|PMID:​3468643]]. +  - Balick DJ, Do R, Cassa CA, Reich D, Sunyaev SR. Dominance of Deleterious Alleles Controls the Response to a Population Bottleneck.\\ PLoS Genet. 2015 Aug 28;​11(8):​e1005436. doi: 10.1371/​journal.pgen.1005436. eCollection 2015 Aug. PubMed [[http://​www.ncbi.nlm.nih.gov/​pubmed/​26317225|PMID:​26317225]]. 
-  - **Cassa CA**, Tong MY, Jordan DM. Large numbers of genetic variants considered to be pathogenic are common in asymptomatic individuals.\\ Hum Mutat 34(9):​1216-20 (2013). PubMed [[http://​www.ncbi.nlm.nih.gov/​pubmed/​23818451|PMID:​23818451]]. +  - Jordan DM, Frangakis SG, Golzio C, Cassa CA, Kurtzberg J; Task Force for Neonatal Genomics, Davis EE, Sunyaev SR, Katsanis N. Identification of cis-suppression of human disease mutations by comparative genomics. \\ Nature. 2015 Aug 13;​524(7564):​225-9. doi: 10.1038/​nature14497. Epub 2015 Jun 29. PubMed [[http://​www.ncbi.nlm.nih.gov/​pubmed/​26123021|PMID:​26123021]]. 
-  - Nusinow DP, Kiezun A, O'​Connell DJ, Chick JM, Yue Y, Maas RL, Gygi SP, **Sunyaev SR**. Network-based inference from complex proteomic mixtures using SNIPE.\\ Bioinformatics 28(23):​3115-22 (2012). PubMed [[http://​www.ncbi.nlm.nih.gov/​pubmed/​23060611|PMID:​23060611]]. +  ​- Francioli LC, Polak PP, Koren A, Menelaou A, Chun S, Renkens I; Genome of the Netherlands Consortium, van Duijn CM, Swertz M, Wijmenga C, van Ommen G, Slagboom PE, Boomsma DI, Ye K, Guryev V, Arndt PF, Kloosterman WP, de Bakker PI, Sunyaev SR. Genome-wide patterns and properties of de novo mutations in humans.\\ Nat Genet. ​47(7):​822-6 ​(2015). PubMed [[http://​www.ncbi.nlm.nih.gov/​pubmed/​25985141|PMID:​25985141]]. 
-  - Kiezun A, Garimella K, Do R, Stitziel NO, Neale BM, McLaren PJ, Gupta N, Sklar P, Sullivan PF, Moran JL, Hultman CM, Lichtenstein P, Magnusson P, Lehner T, Shugart YY, Price AL, de Bakker PI, Purcell SM, **Sunyaev SR**. Exome sequencing and the genetic basis of complex traits.\\ Nat Genet. 44(6):​623-30 (2012). PubMed [[http://​www.ncbi.nlm.nih.gov/​pubmed/​22641211|PMID:​22641211]]. +  - Do R, Balick D, Li H, Adzhubei I, Sunyaev S, Reich D. No evidence that selection has been less effective at removing deleterious mutations in Europeans than in Africans.\\ Nat Genet. 47(2):​126-31 (2015). PubMed [[http://​www.ncbi.nlm.nih.gov/​pubmed/​25581429|PMID:​25581429]]. 
-  - Leshchiner I, Alexa K, Kelsey P, Adzhubei I, Austin-Tse CA, Cooney JD, Anderson H, King MJ, Stottmann RW, Garnaas MK, Ha S, Drummond IA, Paw BH, North TE, Beier DR, Goessling W, **Sunyaev SR**. Mutation mapping and identification by whole-genome sequencing.\\ Genome Res 22(8):​1541-8 (2012). PubMed [[http://​www.ncbi.nlm.nih.gov/​pubmed/​22555591|PMID:​22555591]]. +  - Polak P, Karlić R, Koren A, Thurman R, Sandstrom R, Lawrence MS, Reynolds A, Rynes E, Vlahoviček K, Stamatoyannopoulos JA, Sunyaev SR. Cell-of-origin chromatin organization shapes the mutational landscape of cancer.\\ Nature 518(7539):​360-4 (2015). PubMed [[http://​www.ncbi.nlm.nih.gov/​pubmed/​25693567|PMID:​25693567]]. 
-  - Zuk O, Hechter E, **Sunyaev SR**, Lander ES. The mystery of missing heritability:​ Genetic interactions create phantom heritability.\\ Proc Natl Acad Sci U S A. 109(4):​1193-8 (2012). PubMed [[http://​www.ncbi.nlm.nih.gov/​pubmed/​22223662|PMID:​22223662]] +  - Zuk O, Schaffner SF, Samocha K, Do R, Hechter E, Kathiresan S, Daly MJ, Neale BM, Sunyaev SR, Lander ES.\\ Proc Natl Acad Sci. 111(4):​E455-64 (2014). PubMed [[http://​www.ncbi.nlm.nih.gov/​pubmed/​24443550|PMID:​24443550]]. 
-  - Spirin V, Shpunt A, Seebacher J, Gentzel M, Shevchenko A, Gygi S, **Sunyaev S**. Assigning spectrum-specific P-values to protein identifications by mass spectrometry.\\ Bioinformatics. 27(8):​1128-34 (2011). PubMed [[http://​www.ncbi.nlm.nih.gov/​pubmed/​21349864|PMID:​21349864]]. +  - Polak P, Lawrence MS, Haugen E, Stoletzki N, Stojanov P, Thurman RE, Garraway LA, Mirkin S, Getz G, Stamatoyannopoulos JA, Sunyaev SR. Reduced local mutation density in regulatory DNA of cancer genomes is linked to DNA repair.\\ Nat Biotechnol. 32(1):71-5 (2014). PubMed [[http://​www.ncbi.nlm.nih.gov/​pubmed/​24336318|PMID:​24336318]]. 
-  - Jordan DM, Kiezun A, Baxter SM, Agarwala V, Green RC, Murray MF, Pugh T, Lebo MS, Rehm HL, Funke BH, **Sunyaev SR**. Development and validation of a computational method for assessment of missense variants in hypertrophic cardiomyopathy.\\ Am J Hum Genet. 88(2):​183-92 (2011). PubMed [[http://​www.ncbi.nlm.nih.gov/​pubmed/​21310275|PMID:​21310275]]. +  - Goldstein DB, Allen A, Keebler J, Margulies EH, Petrou S, Petrovski S, Sunyaev S. Sequencing studies in human genetics: design and interpretation.\\ Nat Rev Genet 14(7):​460-70 (2013). PubMed [[http://​www.ncbi.nlm.nih.gov/​pubmed/​23752795|PMID:​23752795]]. 
-  - Price AL, Kryukov GV, de Bakker PI, Purcell SM, Staples J, Wei LJ, **Sunyaev SR**. Pooled association tests for rare variants in exon-resequencing studies.\\ Am J Hum Genet. 86(6):832-8 (2010). PubMed [[http://​www.ncbi.nlm.nih.gov/​pubmed/​20471002|PMID:​20471002]]. +  - Coste B, Houge G, Murray MF, Stitziel N, Bandell M, Giovanni MA, Philippakis A, Hoischen A, Riemer G, Steen U, Steen VM, Mathur J, Cox J, Lebo M, Rehm H, Weiss ST, Wood JN, Maas RL, Sunyaev SR, Patapoutian A. Gain-of-function mutations in the mechanically activated ion channel PIEZO2 cause a subtype of Distal Arthrogryposis.\\ Proc Natl Acad Sci U S A 110(12):​4667-72 (2013). PubMed [[http://​www.ncbi.nlm.nih.gov/​pubmed/​23487782|PMID:​23487782]]. 
-  - Adzhubei IA, Schmidt S, Peshkin L, Ramensky VE, Gerasimova A, Bork P, Kondrashov AS, **Sunyaev SR**. A method and server for predicting damaging missense mutations.\\ Nat Methods. 7(4):248-9 (2010). PubMed [[http://​www.ncbi.nlm.nih.gov/​pubmed/​20354512|PMID:​20354512]].  +  - Kiezun A, Pulit SL, Francioli LC, van Dijk F, Swertz M, Boomsma DI, van Duijn CM, Slagboom PE, van Ommen GJ, Wijmenga C; Genome of the Netherlands Consortium, de Bakker PI, Sunyaev SR. Deleterious alleles in the human genome are on average younger than neutral alleles of the same frequency.\\ PLoS Genet 9(2):​e1003301 (2013). PubMed [[http://​www.ncbi.nlm.nih.gov/​pubmed/​3468643|PMID:​3468643]]. 
-  - Stamatoyannopoulos JA, Adzhubei I, Thurman RE, Kryukov GV, Mirkin SM, **Sunyaev SR**. Human mutation rate associated with DNA replication timing.\\ Nat Genet. 41(4):393-5 (2009). ​ PubMed [[http://​www.ncbi.nlm.nih.gov/​pubmed/​19287383|PMID:​19287383]]. +  - Cassa CA, Tong MY, Jordan DM. Large numbers of genetic variants considered to be pathogenic are common in asymptomatic individuals.\\ Hum Mutat 34(9):​1216-20 (2013). PubMed [[http://​www.ncbi.nlm.nih.gov/​pubmed/​23818451|PMID:​23818451]]. 
-  - Kryukov GV, Shpunt A, Stamatoyannopoulos JA, **Sunyaev SR**. Power of deep, all-exon resequencing for discovery of human trait genes.\\ Proc Natl Acad Sci U S A. 10;​106(10):​3871-6 (2009) PubMed [[http://​www.ncbi.nlm.nih.gov/​pubmed/​19202052|PMID:​19202052]]. +  - Nusinow DP, Kiezun A, O'​Connell DJ, Chick JM, Yue Y, Maas RL, Gygi SP, Sunyaev SR. Network-based inference from complex proteomic mixtures using SNIPE.\\ Bioinformatics 28(23):​3115-22 (2012). PubMed [[http://​www.ncbi.nlm.nih.gov/​pubmed/​23060611|PMID:​23060611]]. 
-  - **Sunyaev SR**, Lugovskoy A, Simon K, Gorelik L. Adaptive mutations in the JC virus protein capsid are associated with progressive multifocal leukoencephalopathy (PML).\\ PLoS Genet. 5(2):​e1000368 (2009) PubMed [[http://​www.ncbi.nlm.nih.gov/​pubmed/​19197354|PMID:​19197354]].+  - Kiezun A, Garimella K, Do R, Stitziel NO, Neale BM, McLaren PJ, Gupta N, Sklar P, Sullivan PF, Moran JL, Hultman CM, Lichtenstein P, Magnusson P, Lehner T, Shugart YY, Price AL, de Bakker PI, Purcell SM, Sunyaev SR. Exome sequencing and the genetic basis of complex traits.\\ Nat Genet. 44(6):​623-30 (2012). PubMed [[http://​www.ncbi.nlm.nih.gov/​pubmed/​22641211|PMID:​22641211]]. 
 +  - Leshchiner I, Alexa K, Kelsey P, Adzhubei I, Austin-Tse CA, Cooney JD, Anderson H, King MJ, Stottmann RW, Garnaas MK, Ha S, Drummond IA, Paw BH, North TE, Beier DR, Goessling W, Sunyaev SR. Mutation mapping and identification by whole-genome sequencing.\\ Genome Res 22(8):​1541-8 (2012). PubMed [[http://​www.ncbi.nlm.nih.gov/​pubmed/​22555591|PMID:​22555591]]. 
 +  - Zuk O, Hechter E, Sunyaev SR, Lander ES. The mystery of missing heritability:​ Genetic interactions create phantom heritability.\\ Proc Natl Acad Sci U S A. 109(4):​1193-8 (2012). PubMed [[http://​www.ncbi.nlm.nih.gov/​pubmed/​22223662|PMID:​22223662]] 
 +  - Spirin V, Shpunt A, Seebacher J, Gentzel M, Shevchenko A, Gygi S, Sunyaev S. Assigning spectrum-specific P-values to protein identifications by mass spectrometry.\\ Bioinformatics. 27(8):​1128-34 (2011). PubMed [[http://​www.ncbi.nlm.nih.gov/​pubmed/​21349864|PMID:​21349864]]. 
 +  - Jordan DM, Kiezun A, Baxter SM, Agarwala V, Green RC, Murray MF, Pugh T, Lebo MS, Rehm HL, Funke BH, Sunyaev SR. Development and validation of a computational method for assessment of missense variants in hypertrophic cardiomyopathy.\\ Am J Hum Genet. 88(2):​183-92 (2011). PubMed [[http://​www.ncbi.nlm.nih.gov/​pubmed/​21310275|PMID:​21310275]]. 
 +  - Price AL, Kryukov GV, de Bakker PI, Purcell SM, Staples J, Wei LJ, Sunyaev SR. Pooled association tests for rare variants in exon-resequencing studies.\\ Am J Hum Genet. 86(6):832-8 (2010). PubMed [[http://​www.ncbi.nlm.nih.gov/​pubmed/​20471002|PMID:​20471002]]. 
 +  - Adzhubei IA, Schmidt S, Peshkin L, Ramensky VE, Gerasimova A, Bork P, Kondrashov AS, Sunyaev SR. A method and server for predicting damaging missense mutations.\\ Nat Methods. 7(4):248-9 (2010). PubMed [[http://​www.ncbi.nlm.nih.gov/​pubmed/​20354512|PMID:​20354512]].  
 +  - Stamatoyannopoulos JA, Adzhubei I, Thurman RE, Kryukov GV, Mirkin SM, Sunyaev SR. Human mutation rate associated with DNA replication timing.\\ Nat Genet. 41(4):393-5 (2009). ​ PubMed [[http://​www.ncbi.nlm.nih.gov/​pubmed/​19287383|PMID:​19287383]]. 
 +  - Kryukov GV, Shpunt A, Stamatoyannopoulos JA, Sunyaev SR. Power of deep, all-exon resequencing for discovery of human trait genes.\\ Proc Natl Acad Sci U S A. 10;​106(10):​3871-6 (2009) PubMed [[http://​www.ncbi.nlm.nih.gov/​pubmed/​19202052|PMID:​19202052]]. 
 +  - Sunyaev SR, Lugovskoy A, Simon K, Gorelik L. Adaptive mutations in the JC virus protein capsid are associated with progressive multifocal leukoencephalopathy (PML).\\ PLoS Genet. 5(2):​e1000368 (2009) PubMed [[http://​www.ncbi.nlm.nih.gov/​pubmed/​19197354|PMID:​19197354]].
  
  
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 ===== All Other Publications Since 2012 ===== ===== All Other Publications Since 2012 =====
  
- +  - Savova V, Pearl EJ, Boke E, Nag A, Adzhubei I, Horb ME, Peshkin L. Transcriptomic insights into genetic diversity of protein-coding genes in X. laevis.\\ Dev Biol. 424(2):​181-188 (2017) PubMed [[https://​www.ncbi.nlm.nih.gov/​pubmed/​28283406|PMID:​28283406]]. 
- +  - Lenz TL, Spirin V, Jordan DM, Sunyaev SR. Excess of deleterious mutations around HLA genes reveals evolutionary cost of balancing selection.\\ Mol Biol Evol. 33(10):​2555-64 (2016) PubMed [[http://​www.ncbi.nlm.nih.gov/​pubmed/​27436009|PMID:​27436009]]. 
-  - Genome of the Netherlands Consortium. Whole-genome sequence variation, population structure and demographic history of the Dutch population. \\ Nat Genet. 46(8):​818-25 (2014) PubMed [[http://​www.ncbi.nlm.nih.gov/​pubmed/​24974849|PMID:​24974849]] ​+  - Palamara PF, Francioli LC, Wilton PR, Genovese G, Gusev A, Finucane HK, Sankararaman S; Genome of the Netherlands Consortium, Sunyaev SR, de Bakker PI, Wakeley J, Pe'er I, Price AL. Leveraging Distant Relatedness to Quantify Human Mutation and Gene-Conversion Rates.\\ Am J Hum Genet. 97(6):​775-89 (2015) PubMed [[http://​www.ncbi.nlm.nih.gov/​pubmed/​26581902|PMID:​26581902]]. 
 +  - Cassa CA, Smith SE, Docken W, Hoffman E, McLaughlin H, Chun S, Leshchiner I, Miraoui H, Raychaudhuri S, Frank NY, Wilson BJ, Sunyaev SR, Maas RL; Brigham Genomic Medicine, Vuzman D. An argument for early genomic sequencing in atypical cases: a WISP3 variant leads to diagnosis of progressive pseudorheumatoid arthropathy of childhood. \\ Rheumatology (Oxford). 2015 Oct 22. pii: kev367. PMID: 2649374444 
 +  - Lenz TL, Deutsch AJ, Han B, Hu X, Okada Y, Eyre S, Knapp M, Zhernakova A, Huizinga TWJ, Abecasis G, Becker J, Boeckxstaens,​ GE, Chen W-M, Franke A, Gladman DD, Gockel I, Gutierrez-Achury J, Martin J, Nair RP, Nöthen MM, Onengut-Gumuscu S, Rahman P, Rantapää-Dahlqvist S, Stuart PE, Tsoi LC, Van Heel DA, Worthington J, Wouters MM, Klareskog L, Elder JT, Gregersen P, Schumacher J, Rich SS, Wijmenga C, Sunyaev SR, de Bakker PIW, Raychaudhuri S. Widespread non-additive and interaction effects within HLA loci modulate the risk of autoimmune diseases. \\ Nat Genet. 47(9):​1085-1090 (2015) PubMed [[http://​www.ncbi.nlm.nih.gov/​pubmed/​26258845|PMID:​26258845]] 
 +  - Chopra SS, Leshchiner I, Duzkale H, McLaughlin H, Giovanni M, Zhang C, Stitziel N, Fingeroth J, Joyce RM, Lebo M, Rehm H, Vuzman D, Maas R, Sunyaev SR, Murray M, Cassa CA. Inherited CHST11/​MIR3922 deletion is associated with a novel recessive syndrome presenting with skeletal malformation and malignant lymphoproliferative disease.\\ Mol Genet Genomic Med. 2015 Sep;​3(5):​413-23. doi: 10.1002/​mgg3.152. Epub 2015 May 10. PMID: 26436107 
 +  - Genome of the Netherlands Consortium. Whole-genome sequence variation, population structure and demographic history of the Dutch population.\\ Nat Genet. 46(8):​818-25 (2014) PubMed [[http://​www.ncbi.nlm.nih.gov/​pubmed/​24974849|PMID:​24974849]] ​
   - MacArthur DG, Manolio TA, Dimmock DP, Rehm HL, Shendure J, Abecasis GR, Adams DR, Altman RB, Antonarakis SE, Ashley EA, Barrett JC, Biesecker LG, Conrad DF, Cooper GM, Cox NJ, Daly MJ, Gerstein MB, Goldstein DB, Hirschhorn JN, Leal SM, Pennacchio LA, Stamatoyannopoulos JA, Sunyaev SR, Valle D, Voight BF, Winckler W, Gunter C. Guidelines for investigating causality of sequence variants in human disease.\\ Nature. 508(7497):​469-76 (2014) PubMed [[http://​www.ncbi.nlm.nih.gov/​pubmed/​24759409|PMID:​24759409]].   - MacArthur DG, Manolio TA, Dimmock DP, Rehm HL, Shendure J, Abecasis GR, Adams DR, Altman RB, Antonarakis SE, Ashley EA, Barrett JC, Biesecker LG, Conrad DF, Cooper GM, Cox NJ, Daly MJ, Gerstein MB, Goldstein DB, Hirschhorn JN, Leal SM, Pennacchio LA, Stamatoyannopoulos JA, Sunyaev SR, Valle D, Voight BF, Winckler W, Gunter C. Guidelines for investigating causality of sequence variants in human disease.\\ Nature. 508(7497):​469-76 (2014) PubMed [[http://​www.ncbi.nlm.nih.gov/​pubmed/​24759409|PMID:​24759409]].
   - Brownstein CA, Beggs AH, Homer N, Merriman B, Yu TW, Flannery KC, DeChene ET, Towne MC, Savage SK, Price EN, Holm IA, Luquette LJ, Lyon E, Majzoub J, Neupert P, McCallie D Jr, Szolovits P, Willard HF, Mendelsohn NJ, Temme R, Finkel RS, Yum SW, Medne L, Sunyaev SR, Adzhubey I, Cassa CA, ... Kohane IS, Margulies DM. An international effort towards developing standards for best practices in analysis, interpretation and reporting of clinical genome sequencing results in the CLARITY Challenge.\\ Genome Biol. 15(3):R53 (2014) PubMed [[http://​www.ncbi.nlm.nih.gov/​pubmed/​24667040|PMID:​24667040]].   - Brownstein CA, Beggs AH, Homer N, Merriman B, Yu TW, Flannery KC, DeChene ET, Towne MC, Savage SK, Price EN, Holm IA, Luquette LJ, Lyon E, Majzoub J, Neupert P, McCallie D Jr, Szolovits P, Willard HF, Mendelsohn NJ, Temme R, Finkel RS, Yum SW, Medne L, Sunyaev SR, Adzhubey I, Cassa CA, ... Kohane IS, Margulies DM. An international effort towards developing standards for best practices in analysis, interpretation and reporting of clinical genome sequencing results in the CLARITY Challenge.\\ Genome Biol. 15(3):R53 (2014) PubMed [[http://​www.ncbi.nlm.nih.gov/​pubmed/​24667040|PMID:​24667040]].
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   - Maurano MT, Humbert R, Rynes E, Thurman RE, Haugen E, Wang H, Reynolds AP, Sandstrom R, Qu H, Brody J, Shafer A, Neri F, Lee K, Kutyavin T, Stehling-Sun S, Johnson AK, Canfield TK, Giste E, Diegel M, Bates D, Hansen RS, Neph S, Sabo PJ, Heimfeld S, Raubitschek A, Ziegler S, Cotsapas C, Sotoodehnia N, Glass I, Sunyaev SR, Kaul R, Stamatoyannopoulos JA. Systematic localization of common disease-associated variation in regulatory DNA.\\ Science 337(6099):​1190-5 (2012). PubMed [[http://​www.ncbi.nlm.nih.gov/​pubmed/​22955828|PMID:​22955828]].   - Maurano MT, Humbert R, Rynes E, Thurman RE, Haugen E, Wang H, Reynolds AP, Sandstrom R, Qu H, Brody J, Shafer A, Neri F, Lee K, Kutyavin T, Stehling-Sun S, Johnson AK, Canfield TK, Giste E, Diegel M, Bates D, Hansen RS, Neph S, Sabo PJ, Heimfeld S, Raubitschek A, Ziegler S, Cotsapas C, Sotoodehnia N, Glass I, Sunyaev SR, Kaul R, Stamatoyannopoulos JA. Systematic localization of common disease-associated variation in regulatory DNA.\\ Science 337(6099):​1190-5 (2012). PubMed [[http://​www.ncbi.nlm.nih.gov/​pubmed/​22955828|PMID:​22955828]].
   - Thurman RE, Rynes E, Humbert R, Vierstra J, Maurano MT, Haugen E, Sheffield NC, Stergachis AB, Wang H, Vernot B, Garg K, John S, Sandstrom R, Bates D, Boatman L, Canfield TK, Diegel M, Dunn D, Ebersol AK, Frum T, Giste E, Johnson AK, Johnson EM, Kutyavin T, Lajoie B, Lee BK, Lee K, London D, Lotakis D, Neph S, Neri F, Nguyen ED, Qu H, Reynolds AP, Roach V, Safi A, Sanchez ME, Sanyal A, Shafer A, Simon JM, Song L, Vong S, Weaver M, Yan Y, Zhang Z, Zhang Z, Lenhard B, Tewari M, Dorschner MO, Hansen RS, Navas PA, Stamatoyannopoulos G, Iyer VR, Lieb JD, Sunyaev SR, Akey JM, Sabo PJ, Kaul R, Furey TS, Dekker J, Crawford GE, Stamatoyannopoulos JA. The accessible chromatin landscape of the human genome.\\ Nature 489(7414):​75-82 (2012). PubMed [[http://​www.ncbi.nlm.nih.gov/​pubmed/​22955617|PMID:​22955617]].   - Thurman RE, Rynes E, Humbert R, Vierstra J, Maurano MT, Haugen E, Sheffield NC, Stergachis AB, Wang H, Vernot B, Garg K, John S, Sandstrom R, Bates D, Boatman L, Canfield TK, Diegel M, Dunn D, Ebersol AK, Frum T, Giste E, Johnson AK, Johnson EM, Kutyavin T, Lajoie B, Lee BK, Lee K, London D, Lotakis D, Neph S, Neri F, Nguyen ED, Qu H, Reynolds AP, Roach V, Safi A, Sanchez ME, Sanyal A, Shafer A, Simon JM, Song L, Vong S, Weaver M, Yan Y, Zhang Z, Zhang Z, Lenhard B, Tewari M, Dorschner MO, Hansen RS, Navas PA, Stamatoyannopoulos G, Iyer VR, Lieb JD, Sunyaev SR, Akey JM, Sabo PJ, Kaul R, Furey TS, Dekker J, Crawford GE, Stamatoyannopoulos JA. The accessible chromatin landscape of the human genome.\\ Nature 489(7414):​75-82 (2012). PubMed [[http://​www.ncbi.nlm.nih.gov/​pubmed/​22955617|PMID:​22955617]].
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