Publications

Export 2169 results:
2022
Matynia A, Wang J, Kim S, Li Y, Dimashkie A, Jiang Z, Hu J, Strom SP, Radu RA, Chen R, Gorin MB. Assessing Variant Causality and Severity Using Retinal Pigment Epithelial Cells Derived from Stargardt Disease Patients. Transl Vis Sci Technol. 2022 ;11(3):33.
Zeng C, Bastarache LA, Tao R, Venner E, Hebbring S, Andujar JD, Bland ST, Crosslin DR, Pratap S, Cooley A, Pacheco JA, Christensen KD, Perez E, Zawatsky CLBlout, Witkowski L, Zouk H, Weng C, Leppig KA, Sleiman PMA, Hakonarson H, Williams MS, Luo Y, Jarvik GP, Green RC, Chung WK, Gharavi AG, Lennon NJ, Rehm HL, Gibbs RA, Peterson JF, Roden DM, Wiesner GL, Denny JC. Association of Pathogenic Variants in Hereditary Cancer Genes With Multiple Diseases. JAMA Oncol. 2022 ;8(6):835-844.
Locke DP, Hillier LDW, Warren WC, Worley KC, Nazareth LV, Muzny DM, Yang S-P, Wang Z, Chinwalla AT, Minx P, Mitreva M, Cook L, Delehaunty KD, Fronick C, Schmidt H, Fulton LA, Fulton RS, Nelson JO, Magrini V, Pohl C, Graves TA, Markovic C, Cree A, Dinh HH, Hume J, Kovar CL, Fowler GR, Lunter G, Meader S, Heger A, Ponting CP, Marques-Bonet T, Alkan C, Chen L, Cheng Z, Kidd JM, Eichler EE, White S, Searle S, Vilella AJ, Chen Y, Flicek P, Ma J, Raney B, Suh B, Burhans R, Herrero J, Haussler D, Faria R, Fernando O, Darré F, Farré D, Gazave E, Oliva M, Navarro A, Roberto R, Capozzi O, Archidiacono N, Valle GDella, Purgato S, Rocchi M, Konkel MK, Walker JA, Ullmer B, Batzer MA, Smit AFA, Hubley R, Casola C, Schrider DR, Hahn MW, Quesada V, Puente XS, Ordoñez GR, López-Otín C, Vinar T, Brejova B, Ratan A, Harris RS, Miller W, Kosiol C, Lawson HA, Taliwal V, Martins AL, Siepel A, Roychoudhury A, Ma X, Degenhardt J, Bustamante CD, Gutenkunst RN, Mailund T, Dutheil JY, Hobolth A, Schierup MH, Ryder OA, Yoshinaga Y, De Jong PJ, Weinstock GM, Rogers J, Mardis ER, Gibbs RA, Wilson RK. Author Correction: Comparative and demographic analysis of orang-utan genomes. Nature. 2022 ;608(7924):E36.
Zhang Y, Chen F, Fonseca NA, He Y, Fujita M, Nakagawa H, Zhang Z, Brazma A, Creighton CJ. Author Correction: High-coverage whole-genome analysis of 1220 cancers reveals hundreds of genes deregulated by rearrangement-mediated cis-regulatory alterations. Nat Commun. 2022 ;13(1):7572.
Reyna MA, Haan D, Paczkowska M, Verbeke LPC, Vazquez M, Kahraman A, Pulido-Tamayo S, Barenboim J, Wadi L, Dhingra P, Shrestha R, Getz G, Lawrence MS, Pedersen JSkou, Rubin MA, Wheeler DA, Brunak S, Izarzugaza JMG, Khurana E, Marchal K, von Mering C, S Sahinalp C, Valencia A, Reimand J, Stuart JM, Raphael BJ. Author Correction: Pathway and network analysis of more than 2500 whole cancer genomes. Nat Commun. 2022 ;13(1):7566.
Zhang Y, Chen F, Chandrashekar DS, Varambally S, Creighton CJ. Author Correction: Proteogenomic characterization of 2002 human cancers reveals pan-cancer molecular subtypes and associated pathways. Nat Commun. 2022 ;13(1):4688.
Chowdhury M, Pedersen BS, Sedlazeck FJ, Quinlan AR, Layer RM. Author Correction: Searching thousands of genomes to classify somatic and novel structural variants using STIX. Nat Methods. 2022 ;19(6):770.
Liu Z, Roberts R, Mercer TR, Xu J, Sedlazeck FJ, Tong W. Author Correction: Towards accurate and reliable resolution of structural variants for clinical diagnosis. Genome Biol. 2022 ;23(1):198.
Wagner J, Olson ND, Harris L, Khan Z, Farek J, Mahmoud M, Stankovic A, Kovacevic V, Yoo B, Miller N, Rosenfeld JA, Ni B, Zarate S, Kirsche M, Aganezov S, Schatz MC, Narzisi G, Byrska-Bishop M, Clarke W, Evani US, Markello C, Shafin K, Zhou X, Sidow A, Bansal V, Ebert P, Marschall T, Lansdorp P, Hanlon V, Mattsson C-A, Barrio AMartinez, Fiddes IT, Xiao C, Fungtammasan A, Chin C-S, Wenger AM, Rowell WJ, Sedlazeck FJ, Carroll A, Salit M, Zook JM. Benchmarking challenging small variants with linked and long reads. Cell Genom. 2022 ;2(5).
Austin-Tse CA, Jobanputra V, Perry DL, Bick D, Taft RJ, Venner E, Gibbs RA, Young T, Barnett S, Belmont JW, Boczek N, Chowdhury S, Ellsworth KA, Guha S, Kulkarni S, Marcou C, Meng L, Murdock DR, Rehman AU, Spiteri E, Thomas-Wilson A, Kearney HM, Rehm HL. Best practices for the interpretation and reporting of clinical whole genome sequencing. NPJ Genom Med. 2022 ;7(1):27.
Khalaf-Nazzal R, Fasham J, Inskeep KA, Blizzard LE, Leslie JS, Wakeling MN, Ubeyratna N, Mitani T, Griffith JL, Baker W, Al-Hijawi F', Keough KC, Gezdirici A, Pena L, Spaeth CG, Turnpenny PD, Walsh JR, Ray R, Neilson A, Kouranova E, Cui X, Curiel DT, Pehlivan D, Akdemir ZCoban, Posey JE, Lupski JR, Dobyns WB, Stottmann RW, Crosby AH, Baple EL. Bi-allelic CAMSAP1 variants cause a clinically recognizable neuronal migration disorder. Am J Hum Genet. 2022 ;109(11):2068-2079.
Marafi D, Fatih JM, Kaiyrzhanov R, Ferla MP, Gijavanekar C, Al-Maraghi A, Liu N, Sites E, Alsaif HS, Al-Owain M, Zakkariah M, El-Anany E, Guliyeva U, Guliyeva S, Gaba C, Haseeb A, Alhashem AM, Danish E, Karageorgou V, Beetz C, Subhi AA, Mullegama SV, Torti E, Sebastin M, Breilyn MSheck, Duberstein S, Abdel-Hamid MS, Mitani T, Du H, Rosenfeld JA, Jhangiani SN, Akdemir ZCoban, Gibbs RA, Taylor JC, Fakhro KA, Hunter JV, Pehlivan D, Zaki MS, Gleeson JG, Maroofian R, Houlden H, Posey JE, V Sutton R, Alkuraya FS, Elsea SH, Lupski JR. Biallelic variants in SLC38A3 encoding a glutamine transporter cause epileptic encephalopathy. Brain. 2022 ;145(3):909-924.
Calame DG, Herman I, Maroofian R, Marshall AE, Donis KCarvalho, Fatih JM, Mitani T, Du H, Grochowski CM, Sousa SB, Gijavanekar C, Bakhtiari S, Ito YA, Rocca C, Hunter JV, V Sutton R, Emrick LT, Boycott KM, Lossos A, Fellig Y, Prus E, Kalish Y, Meiner V, Suerink M, Ruivenkamp C, Muirhead K, Saadi NW, Zaki MS, Bouman A, Barakat TStefan, Skidmore DL, Osmond M, Silva TOliveira, Murphy D, Karimiani EGhayoor, Jamshidi Y, Jaddoa AGhanim, Tajsharghi H, Jin SChih, Abbaszadegan MReza, Ebrahimzadeh-Vesal R, Hosseini S, Alavi S, Bahreini A, Zarean E, Salehi MMehdi, Al-Sannaa NAbbas, Zifarelli G, Bauer P, Robson SC, Coban-Akdemir Z, Travaglini L, Nicita F, Jhangiani SN, Gibbs RA, Posey JE, Kruer MC, Kernohan KD, Saute JAMorales, Houlden H, Vanderver A, Elsea SH, Pehlivan D, Marafi D, Lupski JR. Biallelic Variants in the Ectonucleotidase ENTPD1 Cause a Complex Neurodevelopmental Disorder with Intellectual Disability, Distinct White Matter Abnormalities, and Spastic Paraplegia. Ann Neurol. 2022 ;92(2):304-321.
He S, Granot-Hershkovitz E, Zhang Y, Bressler J, Tarraf W, Yu B, Huang T, Zeng D, Wassertheil-Smoller S, Lamar M, Daviglus M, Marquine MJ, Cai J, Mosley T, Kaplan R, Boerwinkle E, Fornage M, DeCarli C, Kristal B, Gonzalez HM, Sofer T. Blood metabolites predicting mild cognitive impairment in the study of Latinos-investigation of neurocognitive aging (HCHS/SOL). Alzheimers Dement (Amst). 2022 ;14(1):e12259.
Beaudet AL, Gibbs RA. C. Thomas Caskey, M.D. (1938-2022): A remembrance. Am J Hum Genet. 2022 ;109(7):1185-1189.
Baxter SM, Posey JE, Lake NJ, Sobreira N, Chong JX, Buyske S, Blue EE, Chadwick LH, Coban-Akdemir ZH, Doheny KF, Davis CP, Lek M, Wellington C, Jhangiani SN, Gerstein M, Gibbs RA, Lifton RP, MacArthur DG, Matise TC, Lupski JR, Valle D, Bamshad MJ, Hamosh A, Mane S, Nickerson DA, Rehm HL, O'Donnell-Luria A. Centers for Mendelian Genomics: A decade of facilitating gene discovery. Genet Med. 2022 ;24(4):784-797.
Scollon S, Eldomery MK, Reuther J, Lin FY, Potter SL, Desrosiers L, McClain KL, Smith V, Su JMeng-Fen, Venkatramani R, Hu J, Korchina V, Zarrin-Khameh N, Gibbs RA, Muzny DM, Eng C, Roy A, D Parsons W, Plon SE. Clinical and molecular features of pediatric cancer patients with Lynch syndrome. Pediatr Blood Cancer. 2022 ;69(11):e29859.
M Casanova I, Chen R, Garzel LM, Olstad KJ, Kim S, Harris RA, Li Y, Raveendran M, Liang Q, Wang J, Yiu G, Stout JTimothy, Roberts JA, Rogers J, Moshiri A, Thomasy SM. Clinical presentation, treatment, and genetic and histopathological analysis of juvenile cataracts and secondary glaucoma in a rhesus macaque (Macaca mulatta). J Med Primatol. 2022 ;51(2):119-123.
Creighton CJ. Clinical proteomics towards multiomics in cancer. Mass Spectrom Rev. 2022 ;:e21827.
Uddin MDMesbah, Nguyen NQuynh H, Yu B, Brody JA, Pampana A, Nakao T, Fornage M, Bressler J, Sotoodehnia N, Weinstock JS, Honigberg MC, Nachun D, Bhattacharya R, Griffin GK, Chander V, Gibbs RA, Rotter JI, Liu C, Baccarelli AA, Chasman DI, Whitsel EA, Kiel DP, Murabito JM, Boerwinkle E, Ebert BL, Jaiswal S, Floyd JS, Bick AG, Ballantyne CM, Psaty BM, Natarajan P, Conneely KN. Clonal hematopoiesis of indeterminate potential, DNA methylation, and risk for coronary artery disease. Nat Commun. 2022 ;13(1):5350.
Lermi NOzirmak, Gray SB, Bowen CM, Reyes-Uribe L, Dray BK, Deng N, Harris RA, Raveendran M, Benavides F, Hodo CL, Taggart MW, Maresso KColbert, Sinha KM, Rogers J, Vilar E. Comparative molecular genomic analyses of a spontaneous rhesus macaque model of mismatch repair-deficient colorectal cancer. PLoS Genet. 2022 ;18(4):e1010163.
Aganezov S, Yan SM, Soto DC, Kirsche M, Zarate S, Avdeyev P, Taylor DJ, Shafin K, Shumate A, Xiao C, Wagner J, McDaniel J, Olson ND, Sauria MEG, Vollger MR, Rhie A, Meredith M, Martin S, Lee J, Koren S, Rosenfeld JA, Paten B, Layer R, Chin C-S, Sedlazeck FJ, Hansen NF, Miller DE, Phillippy AM, Miga KH, McCoy RC, Dennis MY, Zook JM, Schatz MC. A complete reference genome improves analysis of human genetic variation. Science. 2022 ;376(6588):eabl3533.
Nurk S, Koren S, Rhie A, Rautiainen M, Bzikadze AV, Mikheenko A, Vollger MR, Altemose N, Uralsky L, Gershman A, Aganezov S, Hoyt SJ, Diekhans M, Logsdon GA, Alonge M, Antonarakis SE, Borchers M, Bouffard GG, Brooks SY, Caldas GV, Chen N-C, Cheng H, Chin C-S, Chow W, de Lima LG, Dishuck PC, Durbin R, Dvorkina T, Fiddes IT, Formenti G, Fulton RS, Fungtammasan A, Garrison E, Grady PGS, Graves-Lindsay TA, Hall IM, Hansen NF, Hartley GA, Haukness M, Howe K, Hunkapiller MW, Jain C, Jain M, Jarvis ED, Kerpedjiev P, Kirsche M, Kolmogorov M, Korlach J, Kremitzki M, Li H, Maduro VV, Marschall T, McCartney AM, McDaniel J, Miller DE, Mullikin JC, Myers EW, Olson ND, Paten B, Peluso P, Pevzner PA, Porubsky D, Potapova T, Rogaev EI, Rosenfeld JA, Salzberg SL, Schneider VA, Sedlazeck FJ, Shafin K, Shew CJ, Shumate A, Sims Y, Smit AFA, Soto DC, Sović I, Storer JM, Streets A, Sullivan BA, Thibaud-Nissen F, Torrance J, Wagner J, Walenz BP, Wenger A, Wood JMD, Xiao C, Yan SM, Young AC, Zarate S, Surti U, McCoy RC, Dennis MY, Alexandrov IA, Gerton JL, O'Neill RJ, Timp W, Zook JM, Schatz MC, Eichler EE, Miga KH, Phillippy AM. The complete sequence of a human genome. Science. 2022 ;376(6588):44-53.
Toffoli M, Chen X, Sedlazeck FJ, Lee C-Y, Mullin S, Higgins A, Koletsi S, Garcia-Segura MEmili, Sammler E, Scholz SW, Schapira AHV, Eberle MA, Proukakis C. Comprehensive short and long read sequencing analysis for the Gaucher and Parkinson's disease-associated GBA gene. Commun Biol. 2022 ;5(1):670.
Harris RA, Raveendran M, Lyfoung DT, Sedlazeck FJ, Mahmoud M, Prall TM, Karl JA, Doddapaneni H, Meng Q, Han Y, Muzny DM, Wiseman RW, O'Connor DH, Rogers J. Construction of a new chromosome-scale, long-read reference genome assembly for the Syrian hamster, Mesocricetus auratus. Gigascience. 2022 ;11.