Warren WC, Harris RA, Haukness M, Fiddes IT, Murali SC, Fernandes J, Dishuck PC, Storer JM, Raveendran M, Hillier LW, Porubsky D, Mao Y, Gordon D, Vollger MR, Lewis AP, Munson KM, DeVogelaere E, Armstrong J, Diekhans M, Walker JA, Tomlinson C, Graves-Lindsay TA, Kremitzki M, Salama SR, Audano PA, Escalona M, Maurer NW, Antonacci F, Mercuri L, Maggiolini FAM, Catacchio CR, Underwood JG, O’Connor DH, Sanders AD, Korbel JO, Ferguson B, Kubisch HM, Picker L, Kalin NH, Rosene D, Levine J, Abbott DH, Gray SB, Sanchez MM, Kovacs-Balint ZA, Kemnitz JW, Thomasy SM, Roberts JA, Kinnally EL, Capitanio JP, Skene JHP, Platt M, Cole SA, Green RE, Ventura M, Wiseman RW, Paten B, Batzer MA, Rogers J, Eichler EE. (2020). Sequence diversity analyses of an improved rhesus macaque genome enhance its biomedical utility. Science Dec 18;370(6523):eabc6617. doi: 10.1126/science.abc6617.
Blog Archives
NCKAP1 Disruptive Variants Lead to a Neurodevelopmental Disorder with Core Features of Autism
Guo H, Zhang Q, Dai R, Yu B, Hoekzema K, Tan J, Tan S, Jia X, Chung WK, Hernan R, Alkuraya FS, Alsulaiman A, Al-Muhaizea MA, Lesca G, Pons L, Labalme A, Laux L, Bryant E, Brown NJ, Savva E, Ayres S, Eratne D, Peeters H, Bilan F, Letienne-Cejudo L, Gilbert-Dussardier B, Ruiz-Arana IL, Merlini JM, Boizot A, Bartoloni L, Santoni F, Karlowicz D, McDonald M, Wu H, Hu Z, Chen G, Ou J, Brasch-Andersen C, Fagerberg CR, Dreyer I, Chun-Hui Tsai A, Slegesky V, McGee RB, Daniels B, Sellars EA, Carpenter LA, Schaefer B, Sacoto MJG, Begtrup A, Schnur RE, Punj S, Wentzensen IM, Rhodes L, Pan Q, Bernier RA, Chen C, Eichler EE, Xia K. (2020). NCKAP1 Disruptive Variants Lead to a Neurodevelopmental Disorder with Core Features of Autism. Am J Hum Genet Nov 5;107(5):963-976.
Single-cell strand sequencing of a macaque genome reveals multiple nested inversions and breakpoint reuse during primate evolution
Maggiolini FAM, Sanders AD, Shew CJ, Sulovari A, Mao Y, Puig M, Catacchio CR, Dellino M, Palmisano D, Mercuri L, Bitonto M, Porubský D, Cáceres M, Eichler EE, Ventura M, Dennis MY, Korbel JO, Antonacci F. (2020). Single-cell strand sequencing of a macaque genome reveals multiple nested inversions and breakpoint reuse during primate evolution. Genome Res Nov;30(11):1680-1693.
A Novel Framework for Characterizing Genomic Haplotype Diversity in the Human Immunoglobulin Heavy Chain Locus
Rodriguez OL, Gibson WS, Parks T, Emery M, Powell J, Strahl M, Deikus G, Auckland K, Eichler EE, Marasco WA, Sebra R, Sharp AJ, Smith ML, Bashir A, Watson CT. (2020). A Novel Framework for Characterizing Genomic Haplotype Diversity in the Human Immunoglobulin Heavy Chain Locus. Front Immunol Sep 23;11:2136.
Large-scale targeted sequencing identifies risk genes for neurodevelopmental disorders
Wang T, Hoekzema K, Vecchio D, Wu H, Sulovari A, Coe BP, Gillentine MA, Wilfert AB, Perez-Jurado LA, Kvarnung M, Sleyp Y, Earl RK, Rosenfeld JA, Geisheker MR, Han L, Du B, Barnett C, Thompson E, Shaw M, Carroll R, Friend K, Catford R, Palmer EE, Zou X, Ou J, Li H, Guo H, Gerdts J, Avola E, Calabrese G, Elia M, Greco D, Lindstrand A, Nordgren A, Anderlid BM, Vandeweyer G, Van Dijck A, Van der Aa N, McKenna B, Hancarova M, Bendova S, Havlovicova M, Malerba G, Bernardina BD, Muglia P, van Haeringen A, Hoffer MJV, Franke B, Cappuccio G, Delatycki M, Lockhart PJ, Manning MA, Liu P, Scheffer IE, Brunetti-Pierri N, Rommelse N, Amaral DG, Santen GWE, Trabetti E, Sedláček Z, Michaelson JJ, Pierce K, Courchesne E, Kooy RF; SPARK Consortium, Nordenskjöld M, Romano C, Peeters H, Bernier RA, Gecz J, Xia K, Eichler EE. (2020). Large-scale targeted sequencing identifies risk genes for neurodevelopmental disorders. Nat Commun Oct 1;11(1):4932.
Developmental Predictors of Cognitive and Adaptive Outcomes in Genetic Subtypes of Autism Spectrum Disorder
Arnett AB, Beighley JS, Kurtz-Nelson EC, Hoekzema K, Wang T, Bernier RA, Eichler EE. (2020). Developmental Predictors of Cognitive and Adaptive Outcomes in Genetic Subtypes of Autism Spectrum Disorder. Autism Res Oct;13(10):1659-1669.
HiCanu: accurate assembly of segmental duplications, satellites, and allelic variants from high-fidelity long reads
Nurk S, Walenz BP, Rhie A, Vollger MR, Logsdon GA, Grothe R, Miga KH, Eichler EE, Phillippy AM, Koren S. (2020). HiCanu: accurate assembly of segmental duplications, satellites, and allelic variants from high-fidelity long reads. Genome Res Sep;30(9):1291-1305.
An evolutionary driver of interspersed segmental duplications in primates
Cantsilieris S, Sunkin SM, Johnson ME, Anaclerio F, Huddleston J, Baker C, Dougherty ML, Underwood JG, Sulovari A, Hsieh P, Mao Y, Catacchio CR, Malig M, Welch AE, Sorensen M, Munson KM, Jiang W, Girirajan S, Ventura M, Lamb BT, Conlon RA, Eichler EE. (2020). An evolutionary driver of interspersed segmental duplications in primates. Genome Biol Aug 10;21(1):202.
Evolution of a Human-Specific Tandem Repeat Associated with ALS
Course MM, Gudsnuk K, Smukowski SN, Winston K, Desai N, Ross JP, Sulovari A, Bourassa CV, Spiegelman D, Couthouis J, Yu CE, Tsuang DW, Jayadev S, Kay MA, Gitler AD, Dupre N, Eichler EE, Dion PA, Rouleau GA, Valdmanis PN. (2020). Evolution of a Human-Specific Tandem Repeat Associated with ALS. Am J Hum Genet Sep 3;107(3):445-460.
De novo SMARCA2 variants clustered outside the helicase domain cause a new recognizable syndrome with intellectual disability and blepharophimosis distinct from Nicolaides-Baraitser syndrome
Cappuccio G, Sayou C, Tanno PL, Tisserant E, Bruel AL, Kennani SE, Sá J, Low KJ, Dias C, Havlovicová M, Hancarova M, Eichler EE, Devillard F, Moutton S, Van-Gils J, Dubourg C, Odent S, Gerard B, Piton A, Yamamoto T, Okamoto N, Firth H, Metcalfe K, Moh A, Chapman KA, Aref-Eshghi E, Kerkhof J, Torella A, Nigro V, Perrin L, Piard J, Le Guyader G, Jouan T, Thauvin-Robinet C, Duffourd Y, George-Abraham JK, Buchanan CA, Williams D, Kini U, Wilson K; Telethon Undiagnosed Diseases Program, Sousa SB, Hennekam RCM, Sadikovic B, Thevenon J, Govin J, Vitobello A, Brunetti-Pierri N. (2020). De novo SMARCA2 variants clustered outside the helicase domain cause a new recognizable syndrome with intellectual disability and blepharophimosis distinct from Nicolaides-Baraitser syndrome. Genet Med Nov;22(11):1838-1850.
Nanopore sequencing and the Shasta toolkit enable efficient de novo assembly of eleven human genomes
Shafin K, Pesout T, Lorig-Roach R, Haukness M, Olsen HE, Bosworth C, Armstrong J, Tigyi K, Maurer N, Koren S, Sedlazeck FJ, Marschall T, Mayes S, Costa V, Zook JM, Liu KJ, Kilburn D, Sorensen M, Munson KM, Vollger MR, Monlong J, Garrison E, Eichler EE, Salama S, Haussler D, Green RE, Akeson M, Phillippy A, Miga KH, Carnevali P, Jain M, Paten B. (2020). Nanopore sequencing and the Shasta toolkit enable efficient de novo assembly of eleven human genomes. Nat Biotechnol Sep;38(9):1044-1053.
Telomere-to-telomere assembly of a complete human X chromosome
Miga KH, Koren S, Rhie A, Vollger MR, Gershman A, Bzikadze A, Brooks S, Howe E, Porubsky D, Logsdon GA, Schneider VA, Potapova T, Wood J, Chow W, Armstrong J, Fredrickson J, Pak E, Tigyi K, Kremitzki M, Markovic C, Maduro V, Dutra A, Bouffard GG, Chang AM, Hansen NF, Wilfert AB, Thibaud-Nissen F, Schmitt AD, Belton JM, Selvaraj S, Dennis MY, Soto DC, Sahasrabudhe R, Kaya G, Quick J, Loman NJ, Holmes N, Loose M, Surti U, Risques RA, Graves Lindsay TA, Fulton R, Hall I, Paten B, Howe K, Timp W, Young A, Mullikin JC, Pevzner PA, Gerton JL, Sullivan BA, Eichler EE, Phillippy AM. (2020). Telomere-to-telomere assembly of a complete human X chromosome. Nature Sep;585(7823):79-84.
