Blog Archives
GREGoR: accelerating genomics for rare diseases
Dawood M, Heavner B, Wheeler MM, Ungar RA, LoTempio J, Wiel L, Berger S, Bernstein JA, Chong JX, Délot EC, Eichler EE, Lupski JR, Shojaie A, Talkowski ME, Wagner AH, Wei CL, Wellington C, Wheeler MT; GREGoR Partner Members; Carvalho CMB, Gibbs RA, Gifford CA, May S, Miller DE, Rehm HL, Samocha KE, Sedlazeck FJ, Vilain E, O’Donnell-Luria A, Posey JE, Chadwick LH, Bamshad MJ, Montgomery SB; Genomics Research to Elucidate the Genetics of Rare Diseases (GREGoR) Consortium. (2025). GREGoR: accelerating genomics for rare diseases. Nature Nov;647(8089):331–342. Review.
Locityper enables targeted genotyping of complex polymorphic genes.
Prodanov T, Plender EG, Seebohm G, Meuth SG, Eichler EE, Marschall T. (2025). Locityper enables targeted genotyping of complex polymorphic genes. Nat Genet Nov;57(11):2901–2908.
Structural variation, selection, and diversification of the NPIP gene family from the human pangenome
Dishuck PC, Munson KM, Lewis AP, Dougherty ML, Underwood JG, Harvey WT, Hsieh P, Pastinen T, Eichler EE. (2025). Structural variation, selection, and diversification of the NPIP gene family from the human pangenome. Cell Genom Oct 8;5(10):100977. Featured in AI-generated podcast: “Base by Base Episode 129: Structural variation and diversification of the NPIP gene family from the human pangenome.”
Complex genetic variation in nearly complete human genomes
Logsdon GA, Ebert P, Audano PA, Loftus M, Porubsky D, Ebler J, Yilmaz F, Hallast P, Prodanov T, Yoo D, Paisie CA, Harvey WT, Zhao X, Martino GV, Henglin M, Munson KM, Rabbani K, Chin CS, Gu B, Ashraf H, Scholz S, Austine-Orimoloye O, Balachandran P, Bonder MJ, Cheng H, Chong Z, Crabtree J, Gerstein M, Guethlein LA, Hasenfeld P, Hickey G, Hoekzema K, Hunt SE, Jensen M, Jiang Y, Koren S, Kwon Y, Li C, Li H, Li J, Norman PJ, Oshima KK, Paten B, Phillippy AM, Pollock NR, Rausch T, Rautiainen M, Song Y, Söylev A, Sulovari A, Surapaneni L, Tsapalou V, Zhou W, Zhou Y, Zhu Q, Zody MC, Mills RE, Devine SE, Shi X, Talkowski ME, Chaisson MJP, Dilthey AT, Konkel MK, Korbel JO, Lee C, Beck CR, Eichler EE, Marschall T. (2025). Complex genetic variation in nearly complete human genomes. Nature Aug;644(8076):430-441.
The Platinum Pedigree: a long-read benchmark for genetic variants
Kronenberg Z, Nolan C, Porubsky D, Mokveld T, Rowell WJ, Lee S, Dolzhenko E, Chang PC, Holt JM, Saunders CT, Olson ND, Steely CJ, McGee S, Guarracino A, Koundinya N, Harvey WT, Watkins WS, Munson KM, Hoekzema K, Chua KP, Chen X, Fanslow C, Lambert C, Dashnow H, Garrison E, Smith JD, Lansdorp PM, Zook JM, Carroll A, Jorde LB, Neklason DW, Quinlan AR, Eichler EE, Eberle MA. (2025). The Platinum Pedigree: a long-read benchmark for genetic variants. Nat Methods Aug;22(8):1669-1676.
Predicting Intervention Use in Youth with Rare Variants in Autism-Associated Genes
Benavidez HR, Johansson M, Jones E, Rea H, Kurtz-Nelson EC, Miles C, Whiting A, Eayrs C, Earl R, Bernier RA, Eichler EE, Neuhaus E. (2025). Predicting Intervention Use in Youth with Rare Variants in Autism-Associated Genes. J Autism Dev Disord Aug;55(8):2909-2918. Epub 2024 May 29.
Human de novo mutation rates from a four-generation pedigree reference
. (2025). Human de novo mutation rates from a four-generation pedigree reference. Nature Jul;643(8071):427-436.
SVbyEye: A visual tool to characterize structural variation among whole-genome assemblies
Porubsky D, Guitart X, Yoo D, Dishuck PC, Harvey WT, Eichler EE. (2025). SVbyEye: A visual tool to characterize structural variation among whole-genome assemblies. Bioinformatics Jun 2;41(6):btaf332.
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. (2025). Heterozygous variants disrupting the interaction of ERF with activated ERK1/2 cause microcephaly, developmental delay, and skeletal anomalies. Eur J Hum Genet Jun;33(6):718-726. Epub 2024 Dec 12.
A near telomere-to-telomere phased reference assembly for the male mountain gorilla
Nelson DR, Muvunyi R, Hazzouri KM, Tumushime JC, Nzayisenga G, Julius N, Meert W, Karim L, Coppieters W, Munson KM, Yoo D, Eichler EE, Salehi-Ashtiani K, Twizere JC. (2025). A near telomere-to-telomere phased reference assembly for the male mountain gorilla. Sci Data May 22;12(1):842.
Complete sequencing of ape genomes
. (2025). Complete sequencing of ape genomes. Nature May;641(8062):401-418.

