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Chad Huff, PhD

Present Title & Affiliation

Primary Appointment

Assistant Professor, Department of Epidemiology, Division of OVP, Cancer Prevention and Population Sciences, The University of Texas MD Anderson Cancer Center, Houston, TX

Bio Statement

 

My research is concentrated on understanding human evolution and the genetic basis of human disease through statistical, computational, and population genomics. My work spans a number of human genetics subdisciplines, including disease-gene identification, mutation rate estimation, detection of recent positive selection, and reconstruction of demographic history. I am currently focused on developing new methods to analyze genomic data and by applying these methods to discover novel insights about the genetic basis of human disease, with particular emphasis on identifying and characterizing genes that increase the risk of developing common cancers (colon, breast, head and neck, lung, pancreatic, prostate, and thyroid).

Major Accomplishments

  • Strong publication record, with over 20 peer-reviewed papers, including three papers in Science, two in Nature Genetics, three in Genome Research, and one each in American Journal of Human Genetics, PLoS Genetics, and PNAS
  • Excellent progress in obtaining extramural funding in the first year as an independent investigator, with two established subcontracts, two submitted R01 proposals as a PI, and eight submitted R01 proposals as a co-investigator. 
  •  Principal designer for the algorithm in the Variant Annotation, Analysis, and Search Tool (VAAST), which is a tool designed to identify disease-causing variation from next generation sequence data (Patent application number 61/381,239).
  • Designed algorithm and software for the software package Estimation of Recent Shared Ancestry (ERSA), which greatly expands the range of familial relationships that can be detected from genomic data (Patent application number 61/433,921).

Research Interests

 

*  Identifying intermediate-risk and high-risk cancer susceptibility loci from the analysis of rare genetic variation.
*  Developing methods and software to identify disease-causing genes from sequence data.
*  Developing new methods for pedigree analysis and cryptic relationship identification from genomic data.  
*  Estimating human mutation rates.
*  Uncovering the genetic basis of recent positive selection in humans.
*  Reconstructing human demographic history.

Office Address

The University of Texas MD Anderson Cancer Center
1155 Pressler
Unit 1340
Houston, TX 77030
Phone: 713-563-4957
Email: CHuff1@mdanderson.org

Education & Training

Degree-Granting Education

2008 University of Utah, Salt Lake City, UT, PHD, Biological Anthropology
2004 University of Utah, Salt Lake City, UT, MS, Biological Anthropology
1996 Missouri State University, Springfield, MO, BA, Magna Cum Laude, Computer Information Systems

Experience/Service

Other Appointments/Responsibilities

Software Developer, Whitehead Institute for Biomedical Research, Cambridge, MA, 2001-2002
Database Consultant, iDBA, St. Louis, MO, 2000
Database Architect, Stockell Consulting, St. Louis, MO, 1999-2000
Database Consultant, Oracle, St. Louis, MO, 1998-1999
Database Consultant, MacKenzie and Roth, St. Louis, MO, 1997-1998
Database Administrator, Southwestern Bell, St. Louis, MO, 1996-1997

Honors and Awards

2011-present Ruth L. Kirschstein National Research Service Award (T32)
2010-2012 AAAS/Science program for Excellence in Science
1993-1996 Missouri Higher Education Academic Scholarship
1993-1996 Missouri State University Presidential Scholar
1993 National Merit Scholarship

Professional Memberships

American Association for the Advancement of Science
Member, 2011-present
American Association of Physical Anthropologists
Member, 2007-present
American Society of Human Genetics
Member, 2010-present

Selected Publications

Peer-Reviewed Original Research Articles

1. Hu, Hao, Huff CD. Detecting Statistical Interaction Between Somatic Mutational Events and Germline Variation from Next-Generation Sequence Data. Pac Symp Biocomput. In Press.
2. Wuren T, Simonson TS, Qin G, Xing J, Huff CD, Witherspoon DJ, Jorde LB, Ge RL. Shared and unique signals of high-altitude adaptation in geographically distinct tibetan populations. PLoS One 9(3):e88252, 2014. e-Pub 3/2014. PMCID: PMC3958363.
3. Hu H*, Huff CD* (Co-First Author), Moore B, Flygare S, Reese MG, Yandell M. VAAST 2.0: Improved Variant Classification and Disease-gene Identification Using a Conservation-Controlled Amino Acid Substitution Matrix. Genet Epidemiol 37(6):622-34, 9/2013. e-Pub 7/2013. PMID: 23836555.
4. Xing J, Wuren T, Simonson TS, Watkins WS, Witherspoon DJ, Wu W, Qin G, Huff CD, Jorde LB, Ge RL. Genomic analysis of natural selection and phenotypic variation in high-altitude mongolians. PLoS Genet 9(7):e1003634, 7/2013. e-Pub 7/2013. PMCID: PMC3715426.
5. Tomasic NL, Piterkova L, Huff C, Bilic E, Yoon D, Miasnikova GY, Sergueeva AI, Niu X, Nekhai S, Gordeuk V, Prchal JT. Polycythemia due to Croatian homozygous VHL (571C>G:H191D) mutation has a different phenotype than Chuvash polycythemia (VHL 598C>T:R200W). Haematologica 98(4):560-7, 4/2013. e-Pub 2/2013. PMID: 23403324.
6. 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. Genomic Diversity and Evolution of the Head Crest in the Rock Pigeon. Science 339(6123):1063-7, 3/2013. e-Pub 1/2013. PMID: 23371554.
7. 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. Genetic Risk Factors in two Utah Pedigrees at High Risk for Suicide. Transl Psychiatry 3:e325, 2013. e-Pub 11/2013. PMID: 24252905.
8. Heinzen EL, Swoboda KJ, Hitomi Y, Gurrieri F, Nicole S, de Vries B, Tiziano FD, Fontaine B, Walley NM, Heavin S, Panagiotakaki E, European Alternating Hemiplegia of Childhood (AHC) Genetics Consortium, Nicole S, Gurrieri F, Neri G, de Vries B, Koelewijn S, Kamphorst J, Geilenkirchen M, Pelzer N, Laan L, Haan J, Ferrari M, van den Maagdenberg A, Biobanca e Registro Clinico per l'Emiplegia Alternante (I.B.AHC) Consortium, Zucca C, Bassi MT, Franchini F, Vavassori R, Giannotta M, Gobbi G, Granata T, Nardocci N, De Grandis E, Veneselli E, Stagnaro M, Gurrieri F, Neri G, Vigevano F, European Network for Research on Alternating Hemiplegia (ENRAH) for Small and Medium-sized Enterpriese (SMEs) Consortium, Panagiotakaki E, Oechsler C, Arzimanoglou A, Nicole S, Giannotta M, Gobbi G, Ninan M, Neville B, Ebinger F, Fons C, Campistol J, Kemlink D, Nevsimalova S, Laan L, Peeters-Scholte C, van den Maagdenberg A, Casaer P, Casari G, Sange G, Spiel G, Martinelli Boneschi F, Zucca C, Bassi MT, Schyns T, Crawley F, Poncelin D, Vavassori R, Fiori S, Abiusi E, Di Pietro L, Sweney MT, Newcomb TM, Viollet L, Huff C, Jorde LB, Reyna SP, Murphy KJ, Shianna KV, Gumbs CE, Little L, Silver K, Ptácek LJ, Haan J, Ferrari MD, Bye AM, Herkes GK, Whitelaw CM, Webb D, Lynch BJ, Uldall P, King MD, Scheffer IE, Neri G, Arzimanoglou A, van den Maagdenberg AM, Sisodiya SM, Mikati MA, Goldstein DB. De novo mutations in ATP1A3 cause alternating hemiplegia of childhood. Nat Genet 44(9):1030-4, 7/2012. e-Pub 7/2012. PMID: 22842232.
9. Ge RL, Simonson TS, Cooksey RC, Tanna U, Qin G, Huff CD, Witherspoon DJ, Xing J, Zhengzhong B, Prchal JT, Jorde LB, McClain DA. Metabolic insight into mechanisms of high-altitude adaptation in Tibetans. Mol Genet Metab 106(2):244-7, 6/2012. e-Pub 3/2012. PMID: 22503288.
10. 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. Crohn's disease and genetic hitchhiking at IBD5. Mol Biol Evol 29(1):101-11, 1/2012. e-Pub 8/2011. PMCID: PMC3245542.
11. Watkins W S, Xing J, Huff CD, Witherspoon D, Zhang Y, Perego U, Woodward S, Jorde LB. Genetic analysis of ancestry, admixture and selection in Bolivian and Totonac populations of the New World. BMC Genetics 13(1):39, 2012.
12. 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. Using VAAST to identify an X-linked disorder resulting in lethality in male infants due to N-terminal acetyltransferase deficiency. Am J Hum Genet 89(1):28-43, 7/2011. e-Pub 6/2011. PMCID: PMC3135802.
13. Huff CD*, Witherspoon DJ*, Simonson TS, Xing J, Watkins WS, Zhang Y, Tuohy TM, Neklason DW, Burt RW, Guthery SL, Woodward SR, Jorde LB, *Co-First Author. Maximum-likelihood estimation of recent shared ancestry (ERSA). Genome Res 21(5):768-74, 5/2011. e-Pub 2/2011. PMCID: PMC3083094.
14. Stewart C, Kural D, Strömberg MP, Walker JA, Konkel MK, Stütz AM, Urban AE, Grubert F, Lam HYK, Lee WP, Busby M, Indap AR, Garrison E, Huff CD, Xing J, Snyder MP, Jorde LB, Batzer MA, Korbel JO, Marth GT, 1000 Genomes Project (2011). A comprehensive map of mobile element insertion polymorphisms in humans. PLoS Genetics 7(8):e1002236, 2011.
15. Yandell M*, Huff CD*, Hu H*, Singleton M, Moore B, Xing J, Jorde LB, Reese MG, *Co-First Author. A probabilistic disease-gene finder for personal genomes. Genome Res, 2011.
16. Simonson TS, Xing J, Barrett R, Jerah E, Loa P, Zhang Y, Watkins WS, Witherspoon DJ, Huff CD, Woodward S, Mowry B, Jorde LB. Ancestry of the Iban is predominantly Southeast Asian: genetic evidence from autosomal, mitochondrial, and Y chromosomes. PLoS One 6(1):e16338, 2011. e-Pub 1/2011. PMCID: PMC3031551.
17. 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. Toward a more uniform sampling of human genetic diversity: a survey of worldwide populations by high-density genotyping. Genomics 96(4):199-210, 10/2010. e-Pub 7/2010. PMCID: PMC2945611.
18. Simonson TS, Yang Y, Huff CD, Yun H, Qin G, Witherspoon DJ, Bai Z, Lorenzo FR, Xing J, Jorde LB, Prchal JT, Ge R. Genetic evidence for high-altitude adaptation in Tibet. Science 329(5987):72-5, 7/2010. e-Pub 5/2010. PMID: 20466884.
19. 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, *Co-First Author. Analysis of genetic inheritance in a family quartet by whole-genome sequencing. Science 328(5978):636-9, 4/2010. e-Pub 3/2010. PMCID: PMC3037280.
20. Simonson TS, Zhang Y, Huff CD, Xing J, Watkins WS, Witherspoon DJ, Woodward SR, Jorde LB. Limited distribution of a cardiomyopathy-associated variant in India. Ann Hum Genet 74(2):184-8, 3/2010. e-Pub 2/2010. PMCID: PMC2901538.
21. Huff CD, Xing J, Rogers AR, Witherspoon D, Jorde LB. Mobile elements reveal small population size in the ancient ancestors of Homo sapiens. Proc Natl Acad Sci U S A 107(5):2147-52, 2/2010. e-Pub 1/2010. PMCID: PMC2836654.
22. Ng SB, Buckingham KJ, Lee C, Bigham AW, Tabor HK, Dent KM, Huff CD, Shannon PT, Jabs EW, Nickerson DA, Shendure J, Bamshad MJ. Exome sequencing identifies the cause of a mendelian disorder. Nat Genet 42(1):30-5, 1/2010. e-Pub 11/2009. PMCID: PMC2847889.
23. Huff CD, Harpending HC, Rogers AR. Detecting positive selection from genome scans of linkage disequilibrium. BMC Genomics 11:8, 2010. e-Pub 1/2010. PMCID: PMC2820459.
24. Xing J, Watkins WS, Hu Y, Huff CD, Sabo A, Muzny DM, Bamshad MJ, Gibbs RA, Jorde LB, Yu F. Genetic diversity in India and the inference of Eurasian population expansion. Genome Biol 11(11):R113, 2010. e-Pub 11/2010. PMCID: PMC3156952.
25. Xing J, Zhang Y, Han K, Salem AH, Sen SK, Huff CD, Zhou Q, Kirkness EF, Levy S, Batzer MA, Jorde LB. Mobile elements create structural variation: analysis of a complete human genome. Genome Res 19(9):1516-26, 9/2009. e-Pub 5/2009. PMCID: PMC2752133.
26. Smith SE, Hayes MG, Cabana GS, Huff CD, Coltrain JB, O'Rourke DH. Inferring population continuity versus replacement with aDNA: A cautionary tale from the Aleutian Islands. Hum Biol 81(4):407-726, 8/2009.
27. Rogers AR, Huff CD. Linkage disequilibrium between loci with unknown phase. Genetics 182:834-839, 2009.
28. Rogers AR, Wooding S, Huff CD, Batzer MA, Jorde LB. Ancestral alleles and population origins: inferences depend on mutation rate. Mol Biol Evol 24(4):990-7, 4/2007. e-Pub 1/2007. PMID: 17267423.

Grant & Contract Support

Title: Integrating physiology and genomics to reveal functional adaptation in high altitude Tibetans
Funding Source: NIH/NCI
Role: Principal Investigator-MDACC
Principal Investigator: Tatum Simonson
Duration: 2/1/2015 - 1/31/2019
 
Title: VAAST+: tool for variant prioritization, risk assessment, and disease-gene finding
Funding Source: NIH/NIGMS
Role: Principal Investigator-MDACC
Principal Investigator: Mark Yandell
Duration: 9/1/2013 - 8/31/2017
 
Title: Massively Parallel Sequencing for Familiar Colon Cancer Genes
Funding Source: NIH/NCI
Role: Principal Investigator-MDACC
Principal Investigator: Sean Tavtigian
Duration: 8/1/2012 - 5/31/2017
 
Title: Rare Disease Susceptibility Alleles in Children with Crohn Disease
Funding Source: NIH/NIDDK
Role: Principal Investigator-MDACC
Principal Investigator: Steve Guthery
Duration: 7/1/2012 - 6/30/2015
 
Title: Genetic Analysis of Anticipation in Lynch Syndrome
Funding Source: Cancer Prevention & Research Institute of Texas (CPRIT)
Role: Co-Investigator
Principal Investigator: Marsha Frazier
Duration: 12/1/2010 - 5/31/2014
 
Title: Transdisciplinary Research in Cancer of the Lung (TRICL) ; Area 3: Epidemiologic Architecture of Lung Cancer and Smoking
Funding Source: NIH/NCI
Role: Co-Investigator
Principal Investigator: Christopher Amos
Duration: 7/9/2010 - 6/30/2014

Last updated: 3/3/2014