Li C, Bonder MJ, Syed S, Jensen M; Human Genome Structural Variation Consortium (HGSVC); HGSVC Functional Analysis Working Group; Gerstein MB, Zody MC, Chaisson MJP, Talkowski ME, Marschall T, Korbel JO, Eichler EE, Lee C, Shi X. (2024). An integrative TAD catalog in lymphoblastoid cell lines discloses the functional impact of deletions and insertions in human genomes. Genome Res Dec 23;34(12):2304-2318.
Blog Archives
Heterozygous variants disrupting the interaction of ERF with activated ERK1/2 cause microcephaly, developmental delay, and skeletal anomalies
Micale L, Vourlia A, Fusco C, Pracella R, Karagiannis DC, Nardella G, Vaccaro L, Leone MP, Gramazio A, Dentici ML, Aiello C, Novelli A, Xenou L, Sui Y, Eichler EE, Cacchiarelli D, Mavrothalassitis G, Castori M. (2024). Heterozygous variants disrupting the interaction of ERF with activated ERK1/2 cause microcephaly, developmental delay, and skeletal anomalies. Eur J Hum Genet Dec 12. doi: 10.1038/s41431-024-01721-9. Online ahead of print.
Identification and annotation of centromeric hypomethylated regions with CDR-Finder
Mastrorosa FK, Oshima KK, Rozanski AN, Harvey WT, Eichler EE, Logsdon GA. (2024). Identification and annotation of centromeric hypomethylated regions with CDR-Finder. Bioinformatics Nov 28;40(12):btae733. doi: 10.1093/bioinformatics/btae733.
Independent expansion, selection, and hypervariability of the TBC1D3 gene family in humans
Guitart X, Porubsky D, Yoo D, Dougherty ML, Dishuck PC, Munson KM, Lewis AP, Hoekzema K, Knuth J, Chang S, Pastinen T, Eichler EE. (2024). Independent expansion, selection, and hypervariability of the TBC1D3 gene family in humans. Genome Res Nov 20;34(11):1798-1810.
High-coverage nanopore sequencing of samples from the 1000 Genomes Project to build a comprehensive catalog of human genetic variation
Gustafson JA, Gibson SB, Damaraju N, Zalusky MP, Hoekzema K, Twesigomwe D, Yang L, Snead AA, Richmond PA, De Coster W, Olson ND, Guarracino A, Li Q, Miller AL, Goffena J, Anderson ZB, Storz SH, Ward SA, Sinha M, Gonzaga-Jauregui C, Clarke WE, Basile AO, Corvelo A, Reeves CE, Helland A, Musunuri RL, Revsine M, Patterson KE, Paschal C, Zakarian C, Goodwin S, Jensen TD, Robb E; 1000 Genomes ONT Sequencing Consortium; University of Washington Center for Rare Disease Research (UW-CRDR); Genomics Research to Elucidate the Genetics of Rare Diseases (GREGoR) Consortium; McCombie WR, Sedlazeck FJ, Zook JM, Montgomery SB, Garrison E, Kolmogorov M, Schatz MC, McLaughlin RN Jr, Dashnow H, Zody MC, Loose M, Jain M, Eichler EE, Miller DE. (2024). High-coverage nanopore sequencing of samples from the 1000 Genomes Project to build a comprehensive catalog of human genetic variation. Genome Res Nov 20;34(11):2061-2073.
Deficiency of DDX3X results in neurogenesis defects and abnormal behaviors via dysfunction of the Notch signaling
Duan W, Huang G, Sui Y, Wang K, Yu Y, Chu X, Cao X, Chen L, Liu J, Eichler EE, Xiong B. (2024). Deficiency of DDX3X results in neurogenesis defects and abnormal behaviors via dysfunction of the Notch signaling. Proc Natl Acad Sci U S A Nov 5;121(45):e2404173121. doi: 10.1073/pnas.2404173121. Epub 2024 Oct 29.
3-hour genome sequencing and targeted analysis to rapidly assess genetic risk
Zalusky MP, Gustafson JA, Bohaczuk SC, Mallory B, Reed P, Wenger T, Beckman E, Chang IJ, Paschal CR, Buchan JG, Lockwood CM, Puia-Dumitrescu M, Garalde DR, Guillory J, Markham AJ, Bamshad MJ, Eichler EE, Stergachis AB, Miller DE. (2024). 3-hour genome sequencing and targeted analysis to rapidly assess genetic risk. Genet Med 2024;2:101833. doi: 10.1016/j.gimo.2024.101833. Epub 2024 Feb 24.
Graphasing: phasing diploid genome assembly graphs with single-cell strand sequencing
Henglin M, Ghareghani M, Harvey WT, Porubsky D, Koren S, Eichler EE, Ebert P, Marschall T. (2024). Graphasing: phasing diploid genome assembly graphs with single-cell strand sequencing. Genome Biol Oct 10;25(1):265.
AGAP duplicons associate with structural diversity at Chromosome 10q11.22
Fornezza S, Delvecchio VS, Harvey WT, Dishuck PC, Eichler EE, Giannuzzi G. (2024). AGAP duplicons associate with structural diversity at Chromosome 10q11.22. Genome Res Oct 29;34(10):1487–1499.
Loss-of-function variants in CUL3 cause a syndromic neurodevelopmental disorder
Blackburn PR, Ebstein F, Hsieh TC, Motta M, Radio FC, Herkert JC, Rinne T, Thiffault I, Rapp M, Alders M, Maas S, Gerard B, Smol T, Vincent-Delorme C, Cogné B, Isidor B, Vincent M, Bachmann-Gagescu R, Rauch A, Joset P, Ferrero GB, Ciolfi A, Husson T, Guerrot AM, Bacino C, Macmurdo C, Thompson SS, Rosenfeld JA, Faivre L, Mau-Them FT, Deb W, Vignard V, Agrawal PB, Madden JA, Goldenberg A, Lecoquierre F, Zech M, Prokisch H, Necpál J, Jech R, Winkelmann J, Koprušáková MT, Konstantopoulou V, Younce JR, Shinawi M, Mighton C, Fung C, Morel CF, Lerner-Ellis J, DiTroia S, Barth M, Bonneau D, Krapels I, Stegmann APA, van der Schoot V, Brunet T, Bußmann C, Mignot C, Zampino G, Wortmann SB, Mayr JA, Feichtinger RG, Courtin T, Ravelli C, Keren B, Ziegler A, Hasadsri L, Pichurin PN, Klee EW, Grand K, Sanchez-Lara PA, Krüger E, Bézieau S, Klinkhammer H, Krawitz PM, Eichler EE, Tartaglia M, Küry S, Wang T. (2024). Loss-of-function variants in CUL3 cause a syndromic neurodevelopmental disorder. Ann Neurol Sep 20. doi: 10.1002/ana.27077. Online ahead of print.
Structural and genetic diversity in the secreted mucins MUC5AC and MUC5B
Plender EG, Prodanov T, Hsieh P, Nizamis E, Harvey WT, Sulovari A, Munson KM, Kaufman EJ, O’Neal WK, Valdmanis PN, Marschall T, Bloom JD, Eichler EE. (2024). Structural and genetic diversity in the secreted mucins MUC5AC and MUC5B. Am J Hum Genet Aug 8;111(8):1700-1716.
Visual and auditory attention in individuals with DYRK1A and SCN2A disruptive variants
Hudac CM, Dommer K, Mahony M, DesChamps TD, Cairney B, Earl R, Kurtz-Nelson EC, Bradshaw J, Bernier RA, Eichler EE, Neuhaus E, Webb SJ, Shic F. (2024). Visual and auditory attention in individuals with DYRK1A and SCN2A disruptive variants. Autism Res Jul 30. doi: 10.1002/aur.3202. Online ahead of print.
