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Items: 43

1.

Assessing the performance of in silico methods for predicting the pathogenicity of variants in the gene CHEK2, among Hispanic females with breast cancer.

Voskanian A, Katsonis P, Lichtarge O, Pejaver V, Radivojac P, Mooney SD, Capriotti E, Bromberg Y, Wang Y, Miller M, Martelli PL, Savojardo C, Babbi G, Casadio R, Cao Y, Sun Y, Shen Y, Garg A, Pal D, Yu Y, Huff CD, Tavtigian SV, Young E, Neuhausen SL, Ziv E, Pal LR, Andreoletti G, Brenner SE, Kann MG.

Hum Mutat. 2019 Sep;40(9):1612-1622. doi: 10.1002/humu.23849. Epub 2019 Aug 17.

PMID:
31241222
2.

Association Between Birth Defects and Cancer Risk Among Children and Adolescents in a Population-Based Assessment of 10 Million Live Births.

Lupo PJ, Schraw JM, Desrosiers TA, Nembhard WN, Langlois PH, Canfield MA, Copeland G, Meyer RE, Brown AL, Chambers TM, Sok P, Danysh HE, Carozza SE, Sisoudiya SD, Hilsenbeck SG, Janitz AE, Oster ME, Scheuerle AE, Schiffman JD, Luo C, Mian A, Mueller BA, Huff CD, Rasmussen SA, Scheurer ME, Plon SE.

JAMA Oncol. 2019 Jun 20. doi: 10.1001/jamaoncol.2019.1215. [Epub ahead of print] Erratum in: JAMA Oncol. 2019 Aug 1;5(8):1232.

PMID:
31219523
3.

ALPK1 missense pathogenic variant in five families leads to ROSAH syndrome, an ocular multisystem autosomal dominant disorder.

Williams LB, Javed A, Sabri A, Morgan DJ, Huff CD, Grigg JR, Heng XT, Khng AJ, Hollink IHIM, Morrison MA, Owen LA, Anderson K, Kinard K, Greenlees R, Novacic D, Nida Sen H, Zein WM, Rodgers GM, Vitale AT, Haider NB, Hillmer AM, Ng PC, Shankaracharya, Cheng A, Zheng L, Gillies MC, van Slegtenhorst M, van Hagen PM, Missotten TOAR, Farley GL, Polo M, Malatack J, Curtin J, Martin F, Arbuckle S, Alexander SI, Chircop M, Davila S, Digre KB, Jamieson RV, DeAngelis MM.

Genet Med. 2019 Sep;21(9):2103-2115. doi: 10.1038/s41436-019-0476-3. Epub 2019 Apr 10.

PMID:
30967659
4.

Functionally oriented analysis of cardiometabolic traits in a trans-ethnic sample.

Petty LE, Highland HM, Gamazon ER, Hu H, Karhade M, Chen HH, de Vries PS, Grove ML, Aguilar D, Bell GI, Huff CD, Hanis CL, Doddapaneni H, Munzy DM, Gibbs RA, Ma J, Parra EJ, Cruz M, Valladares-Salgado A, Arking DE, Barbeira A, Im HK, Morrison AC, Boerwinkle E, Below JE.

Hum Mol Genet. 2019 Apr 1;28(7):1212-1224. doi: 10.1093/hmg/ddy435.

5.

Introgression of regulatory alleles and a missense coding mutation drive plumage pattern diversity in the rock pigeon.

Vickrey AI, Bruders R, Kronenberg Z, Mackey E, Bohlender RJ, Maclary ET, Maynez R, Osborne EJ, Johnson KP, Huff CD, Yandell M, Shapiro MD.

Elife. 2018 Jul 17;7. pii: e34803. doi: 10.7554/eLife.34803.

6.

Integrated case-control and somatic-germline interaction analyses of melanoma susceptibility genes.

Yu Y, Hu H, Chen JS, Hu F, Fowler J, Scheet P, Zhao H, Huff CD.

Biochim Biophys Acta Mol Basis Dis. 2018 Jun;1864(6 Pt B):2247-2254. doi: 10.1016/j.bbadis.2018.01.007. Epub 2018 Jan 6.

7.

XPAT: a toolkit to conduct cross-platform association studies with heterogeneous sequencing datasets.

Yu Y, Hu H, Bohlender RJ, Hu F, Chen JS, Holt C, Fowler J, Guthery SL, Scheet P, Hildebrandt MAT, Yandell M, Huff CD.

Nucleic Acids Res. 2018 Apr 6;46(6):e32. doi: 10.1093/nar/gkx1280.

8.

Reply to Mafessoni and Prüfer: Inferences with and without singleton site patterns.

Rogers AR, Bohlender RJ, Huff CD.

Proc Natl Acad Sci U S A. 2017 Nov 28;114(48):E10258-E10260. doi: 10.1073/pnas.1717085114. Epub 2017 Nov 14. No abstract available.

9.

Two Novel Susceptibility Loci for Prostate Cancer in Men of African Ancestry.

Conti DV, Wang K, Sheng X, Bensen JT, Hazelett DJ, Cook MB, Ingles SA, Kittles RA, Strom SS, Rybicki BA, Nemesure B, Isaacs WB, Stanford JL, Zheng W, Sanderson M, John EM, Park JY, Xu J, Stevens VL, Berndt SI, Huff CD, Wang Z, Yeboah ED, Tettey Y, Biritwum RB, Adjei AA, Tay E, Truelove A, Niwa S, Sellers TA, Yamoah K, Murphy AB, Crawford DC, Gapstur SM, Bush WS, Aldrich MC, Cussenot O, Petrovics G, Cullen J, Neslund-Dudas C, Stern MC, Jarai ZK, Govindasami K, Chokkalingam AP, Hsing AW, Goodman PJ, Hoffmann T, Drake BF, Hu JJ, Clark PE, Van Den Eeden SK, Blanchet P, Fowke JH, Casey G, Hennis AJM, Han Y, Lubwama A, Thompson IM Jr, Leach R, Easton DF, Schumacher F, Van den Berg DJ, Gundell SM, Stram A, Wan P, Xia L, Pooler LC, Mohler JL, Fontham ETH, Smith GJ, Taylor JA, Srivastava S, Eeles RA, Carpten J, Kibel AS, Multigner L, Parent ME, Menegaux F, Cancel-Tassin G, Klein EA, Brureau L, Stram DO, Watya S, Chanock SJ, Witte JS, Blot WJ, Henderson BE, Haiman CA; PRACTICAL/ELLIPSE Consortium.

J Natl Cancer Inst. 2017 Aug 1;109(8). doi: 10.1093/jnci/djx084.

10.

Early history of Neanderthals and Denisovans.

Rogers AR, Bohlender RJ, Huff CD.

Proc Natl Acad Sci U S A. 2017 Sep 12;114(37):9859-9863. doi: 10.1073/pnas.1706426114. Epub 2017 Aug 7.

11.

Evolutionary history of Tibetans inferred from whole-genome sequencing.

Hu H, Petousi N, Glusman G, Yu Y, Bohlender R, Tashi T, Downie JM, Roach JC, Cole AM, Lorenzo FR, Rogers AR, Brunkow ME, Cavalleri G, Hood L, Alpatty SM, Prchal JT, Jorde LB, Robbins PA, Simonson TS, Huff CD.

PLoS Genet. 2017 Apr 27;13(4):e1006675. doi: 10.1371/journal.pgen.1006675. eCollection 2017 Apr.

12.

Discovery and fine-mapping of adiposity loci using high density imputation of genome-wide association studies in individuals of African ancestry: African Ancestry Anthropometry Genetics Consortium.

Ng MCY, Graff M, Lu Y, Justice AE, Mudgal P, Liu CT, Young K, Yanek LR, Feitosa MF, Wojczynski MK, Rand K, Brody JA, Cade BE, Dimitrov L, Duan Q, Guo X, Lange LA, Nalls MA, Okut H, Tajuddin SM, Tayo BO, Vedantam S, Bradfield JP, Chen G, Chen WM, Chesi A, Irvin MR, Padhukasahasram B, Smith JA, Zheng W, Allison MA, Ambrosone CB, Bandera EV, Bartz TM, Berndt SI, Bernstein L, Blot WJ, Bottinger EP, Carpten J, Chanock SJ, Chen YI, Conti DV, Cooper RS, Fornage M, Freedman BI, Garcia M, Goodman PJ, Hsu YH, Hu J, Huff CD, Ingles SA, John EM, Kittles R, Klein E, Li J, McKnight B, Nayak U, Nemesure B, Ogunniyi A, Olshan A, Press MF, Rohde R, Rybicki BA, Salako B, Sanderson M, Shao Y, Siscovick DS, Stanford JL, Stevens VL, Stram A, Strom SS, Vaidya D, Witte JS, Yao J, Zhu X, Ziegler RG, Zonderman AB, Adeyemo A, Ambs S, Cushman M, Faul JD, Hakonarson H, Levin AM, Nathanson KL, Ware EB, Weir DR, Zhao W, Zhi D; Bone Mineral Density in Childhood Study (BMDCS) Group, Arnett DK, Grant SFA, Kardia SLR, Oloapde OI, Rao DC, Rotimi CN, Sale MM, Williams LK, Zemel BS, Becker DM, Borecki IB, Evans MK, Harris TB, Hirschhorn JN, Li Y, Patel SR, Psaty BM, Rotter JI, Wilson JG, Bowden DW, Cupples LA, Haiman CA, Loos RJF, North KE.

PLoS Genet. 2017 Apr 21;13(4):e1006719. doi: 10.1371/journal.pgen.1006719. eCollection 2017 Apr.

13.

Gain-of-function EGLN1 prolyl hydroxylase (PHD2 D4E:C127S) in combination with EPAS1 (HIF-2α) polymorphism lowers hemoglobin concentration in Tibetan highlanders.

Tashi T, Scott Reading N, Wuren T, Zhang X, Moore LG, Hu H, Tang F, Shestakova A, Lorenzo F, Burjanivova T, Koul P, Guchhait P, Wittwer CT, Julian CG, Shah B, Huff CD, Gordeuk VR, Prchal JT, Ge R.

J Mol Med (Berl). 2017 Jun;95(6):665-670. doi: 10.1007/s00109-017-1519-3. Epub 2017 Feb 23.

PMID:
28233034
14.

Evolutionary selected Tibetan variants of HIF pathway and risk of lung cancer.

Lanikova L, Reading NS, Hu H, Tashi T, Burjanivova T, Shestakova A, Siwakoti B, Thakur BK, Pun CB, Sapkota A, Abdelaziz S, Feng BJ, Huff CD, Hashibe M, Prchal JT.

Oncotarget. 2017 Feb 14;8(7):11739-11747. doi: 10.18632/oncotarget.14340.

15.

VARPRISM: incorporating variant prioritization in tests of de novo mutation association.

Hu H, Coon H, Li M, Yandell M, Huff CD.

Genome Med. 2016 Aug 25;8(1):91. doi: 10.1186/s13073-016-0341-9.

16.

PADRE: Pedigree-Aware Distant-Relationship Estimation.

Staples J, Witherspoon DJ, Jorde LB, Nickerson DA; University of Washington Center for Mendelian Genomics, Below JE, Huff CD.

Am J Hum Genet. 2016 Jul 7;99(1):154-62. doi: 10.1016/j.ajhg.2016.05.020. Epub 2016 Jun 30.

17.

The Relationship between Native American Ancestry, Body Mass Index and Diabetes Risk among Mexican-Americans.

Hu H, Huff CD, Yamamura Y, Wu X, Strom SS.

PLoS One. 2015 Oct 26;10(10):e0141260. doi: 10.1371/journal.pone.0141260. eCollection 2015.

18.

Adaptive genetic changes related to haemoglobin concentration in native high-altitude Tibetans.

Simonson TS, Huff CD, Witherspoon DJ, Prchal JT, Jorde LB.

Exp Physiol. 2015 Nov;100(11):1263-8. doi: 10.1113/EP085035. Review.

19.

Rare mutations in RINT1 predispose carriers to breast and Lynch syndrome-spectrum cancers.

Park DJ, Tao K, Le Calvez-Kelm F, Nguyen-Dumont T, Robinot N, Hammet F, Odefrey F, Tsimiklis H, Teo ZL, Thingholm LB, Young EL, Voegele C, Lonie A, Pope BJ, Roane TC, Bell R, Hu H, Shankaracharya, Huff CD, Ellis J, Li J, Makunin IV, John EM, Andrulis IL, Terry MB, Daly M, Buys SS, Snyder C, Lynch HT, Devilee P, Giles GG, Hopper JL, Feng BJ, Lesueur F, Tavtigian SV, Southey MC, Goldgar DE.

Cancer Discov. 2014 Jul;4(7):804-15. doi: 10.1158/2159-8290.CD-14-0212. Epub 2014 May 2.

20.

A unified test of linkage analysis and rare-variant association for analysis of pedigree sequence data.

Hu H, Roach JC, Coon H, Guthery SL, Voelkerding KV, Margraf RL, Durtschi JD, Tavtigian SV, Shankaracharya, Wu W, Scheet P, Wang S, Xing J, Glusman G, Hubley R, Li H, Garg V, Moore B, Hood L, Galas DJ, Srivastava D, Reese MG, Jorde LB, Yandell M, Huff CD.

Nat Biotechnol. 2014 Jul;32(7):663-9. doi: 10.1038/nbt.2895. Epub 2014 May 18.

21.

Phevor combines multiple biomedical ontologies for accurate identification of disease-causing alleles in single individuals and small nuclear families.

Singleton MV, Guthery SL, Voelkerding KV, Chen K, Kennedy B, Margraf RL, Durtschi J, Eilbeck K, Reese MG, Jorde LB, Huff CD, Yandell M.

Am J Hum Genet. 2014 Apr 3;94(4):599-610. doi: 10.1016/j.ajhg.2014.03.010.

22.

Shared and unique signals of high-altitude adaptation in geographically distinct Tibetan populations.

Wuren T, Simonson TS, Qin G, Xing J, Huff CD, Witherspoon DJ, Jorde LB, Ge RL.

PLoS One. 2014 Mar 18;9(3):e88252. doi: 10.1371/journal.pone.0088252. eCollection 2014.

23.

Relationship estimation from whole-genome sequence data.

Li H, Glusman G, Hu H, Shankaracharya, Caballero J, Hubley R, Witherspoon D, Guthery SL, Mauldin DE, Jorde LB, Hood L, Roach JC, Huff CD.

PLoS Genet. 2014 Jan 30;10(1):e1004144. doi: 10.1371/journal.pgen.1004144. eCollection 2014 Jan.

25.

Genetic risk factors in two Utah pedigrees at high risk for suicide.

Coon H, Darlington T, Pimentel R, Smith KR, Huff CD, Hu H, Jerominski L, Hansen J, Klein M, Callor WB, Byrd J, Bakian A, Crowell SE, McMahon WM, Rajamanickam V, Camp NJ, McGlade E, Yurgelun-Todd D, Grey T, Gray D.

Transl Psychiatry. 2013 Nov 19;3:e325. doi: 10.1038/tp.2013.100.

26.

Genomic analysis of natural selection and phenotypic variation in high-altitude mongolians.

Xing J, Wuren T, Simonson TS, Watkins WS, Witherspoon DJ, Wu W, Qin G, Huff CD, Jorde LB, Ge RL.

PLoS Genet. 2013;9(7):e1003634. doi: 10.1371/journal.pgen.1003634. Epub 2013 Jul 18.

27.

VAAST 2.0: improved variant classification and disease-gene identification using a conservation-controlled amino acid substitution matrix.

Hu H, Huff CD, Moore B, Flygare S, Reese MG, Yandell M.

Genet Epidemiol. 2013 Sep;37(6):622-34. doi: 10.1002/gepi.21743. Epub 2013 Jul 8.

28.

Genomic diversity and evolution of the head crest in the rock pigeon.

Shapiro MD, Kronenberg Z, Li C, Domyan ET, Pan H, Campbell M, Tan H, Huff CD, Hu H, Vickrey AI, Nielsen SC, Stringham SA, Hu H, Willerslev E, Gilbert MT, Yandell M, Zhang G, Wang J.

Science. 2013 Mar 1;339(6123):1063-7. doi: 10.1126/science.1230422. Epub 2013 Jan 31.

29.

Metabolic insight into mechanisms of high-altitude adaptation in Tibetans.

Ge RL, Simonson TS, Cooksey RC, Tanna U, Qin G, Huff CD, Witherspoon DJ, Xing J, Zhengzhong B, Prchal JT, Jorde LB, McClain DA.

Mol Genet Metab. 2012 Jun;106(2):244-7. doi: 10.1016/j.ymgme.2012.03.003. Epub 2012 Mar 17.

30.

Crohn's disease and genetic hitchhiking at IBD5.

Huff CD, Witherspoon DJ, Zhang Y, Gatenbee C, Denson LA, Kugathasan S, Hakonarson H, Whiting A, Davis CT, Wu W, Xing J, Watkins WS, Bamshad MJ, Bradfield JP, Bulayeva K, Simonson TS, Jorde LB, Guthery SL.

Mol Biol Evol. 2012 Jan;29(1):101-11. doi: 10.1093/molbev/msr151. Epub 2011 Aug 4.

31.

Using VAAST to identify an X-linked disorder resulting in lethality in male infants due to N-terminal acetyltransferase deficiency.

Rope AF, Wang K, Evjenth R, Xing J, Johnston JJ, Swensen JJ, Johnson WE, Moore B, Huff CD, Bird LM, Carey JC, Opitz JM, Stevens CA, Jiang T, Schank C, Fain HD, Robison R, Dalley B, Chin S, South ST, Pysher TJ, Jorde LB, Hakonarson H, Lillehaug JR, Biesecker LG, Yandell M, Arnesen T, Lyon GJ.

Am J Hum Genet. 2011 Jul 15;89(1):28-43. doi: 10.1016/j.ajhg.2011.05.017. Epub 2011 Jun 23. Erratum in: Am J Hum Genet. 2011 Aug 12;89(2):345.

32.

Maximum-likelihood estimation of recent shared ancestry (ERSA).

Huff CD, Witherspoon DJ, Simonson TS, Xing J, Watkins WS, Zhang Y, Tuohy TM, Neklason DW, Burt RW, Guthery SL, Woodward SR, Jorde LB.

Genome Res. 2011 May;21(5):768-74. doi: 10.1101/gr.115972.110. Epub 2011 Feb 8.

33.

Ancestry of the Iban is predominantly Southeast Asian: genetic evidence from autosomal, mitochondrial, and Y chromosomes.

Simonson TS, Xing J, Barrett R, Jerah E, Loa P, Zhang Y, Watkins WS, Witherspoon DJ, Huff CD, Woodward S, Mowry B, Jorde LB.

PLoS One. 2011 Jan 31;6(1):e16338. doi: 10.1371/journal.pone.0016338.

34.

Genetic diversity in India and the inference of Eurasian population expansion.

Xing J, Watkins WS, Hu Y, Huff CD, Sabo A, Muzny DM, Bamshad MJ, Gibbs RA, Jorde LB, Yu F.

Genome Biol. 2010;11(11):R113. doi: 10.1186/gb-2010-11-11-r113. Epub 2010 Nov 24.

35.

Toward a more uniform sampling of human genetic diversity: a survey of worldwide populations by high-density genotyping.

Xing J, Watkins WS, Shlien A, Walker E, Huff CD, Witherspoon DJ, Zhang Y, Simonson TS, Weiss RB, Schiffman JD, Malkin D, Woodward SR, Jorde LB.

Genomics. 2010 Oct;96(4):199-210. doi: 10.1016/j.ygeno.2010.07.004. Epub 2010 Jul 16.

36.

Genetic evidence for high-altitude adaptation in Tibet.

Simonson TS, Yang Y, Huff CD, Yun H, Qin G, Witherspoon DJ, Bai Z, Lorenzo FR, Xing J, Jorde LB, Prchal JT, Ge R.

Science. 2010 Jul 2;329(5987):72-5. doi: 10.1126/science.1189406. Epub 2010 May 13.

37.

Analysis of genetic inheritance in a family quartet by whole-genome sequencing.

Roach JC, Glusman G, Smit AF, Huff CD, Hubley R, Shannon PT, Rowen L, Pant KP, Goodman N, Bamshad M, Shendure J, Drmanac R, Jorde LB, Hood L, Galas DJ.

Science. 2010 Apr 30;328(5978):636-9. doi: 10.1126/science.1186802. Epub 2010 Mar 10.

38.

Limited distribution of a cardiomyopathy-associated variant in India.

Simonson TS, Zhang Y, Huff CD, Xing J, Watkins WS, Witherspoon DJ, Woodward SR, Jorde LB.

Ann Hum Genet. 2010 Mar;74(2):184-8. doi: 10.1111/j.1469-1809.2010.00561.x. Epub 2010 Feb 18.

39.

Mobile elements reveal small population size in the ancient ancestors of Homo sapiens.

Huff CD, Xing J, Rogers AR, Witherspoon D, Jorde LB.

Proc Natl Acad Sci U S A. 2010 Feb 2;107(5):2147-52. doi: 10.1073/pnas.0909000107. Epub 2010 Jan 19.

40.

Detecting positive selection from genome scans of linkage disequilibrium.

Huff CD, Harpending HC, Rogers AR.

BMC Genomics. 2010 Jan 5;11:8. doi: 10.1186/1471-2164-11-8.

41.

Exome sequencing identifies the cause of a mendelian disorder.

Ng SB, Buckingham KJ, Lee C, Bigham AW, Tabor HK, Dent KM, Huff CD, Shannon PT, Jabs EW, Nickerson DA, Shendure J, Bamshad MJ.

Nat Genet. 2010 Jan;42(1):30-5. doi: 10.1038/ng.499. Epub 2009 Nov 13.

42.

Mobile elements create structural variation: analysis of a complete human genome.

Xing J, Zhang Y, Han K, Salem AH, Sen SK, Huff CD, Zhou Q, Kirkness EF, Levy S, Batzer MA, Jorde LB.

Genome Res. 2009 Sep;19(9):1516-26. doi: 10.1101/gr.091827.109. Epub 2009 May 13.

43.

Ancestral alleles and population origins: inferences depend on mutation rate.

Rogers AR, Wooding S, Huff CD, Batzer MA, Jorde LB.

Mol Biol Evol. 2007 Apr;24(4):990-7. Epub 2007 Jan 30.

PMID:
17267423

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