Ke Hao
Education
Doctor of Science
Bachelor of Science
Department of Genetics and Genomic Sciences
Institute of Genomics and Multiscale Biology
Mount Sinai School of Medicine
One Gustave L. Levy Place – Box 1498
New York, NY 10029-6574
Tel: (212) 659-8534; Fax: (646) 537-8660
Email: ke.hao@mssm.edu
1998-2003 Program for Population Genetics
Harvard University, Massachusetts, USA
1993-1997 Department of Biological Sciences and Biotechnology
Tsinghua University, Beijing, China
Research Experience
2012 – present
Associate Professor
Department of Genetics and Genomic Sciences
Mount Sinai School of Medicine
Research Projects:
1. Cancer genomic and causal network of hepatocellular carcinoma and
cholangiocarcinoma
2. Genetic study of RNA editing in brain, depression and suicide
3. COPD among subjects with lung cancer
2007 - 2012
Research Fellow, Rosetta Impharmatics / Merck Research Labs
Projects:
1. Systematic characterization of genetic architecture of gene expression (eQTLs) in
human tissues (Lung, Liver, Adipose, Blood, Brain, etc.)
2. Cancer genomics
 Integrated approaches in hepatocellular carcinoma: clinicopathogical
parameters, normal-tumor pairs, expression/SNP arrays, CNV, wholegenome DNA-sequencing and transcriptome-sequencing
 Gene-expression and exome-sequencing in breast and ovarian cancer
3. Pharmacogenomics
 Identification of biomarkers and construction of classifiers in predicting
liver cancer prognostics
 Pharmacogenetics study on efficacy of leukotriene inhibitors
 Genetic basis of drug induced liver injury (severe adverse event) using
exome-sequencing approach
4. Association study on complex human disease using exome-sequencing approach
 Hyperlipidemia
5. Meta-genome sequencing study on inflammatory bowel disease
 Disease status and treatment efficacy of biologics
 Meta-genome sequencing in stool sample and exome-seq on human host
6. Dissecting complex human diseases using GWAS and systems biology approach
(Asthma, Diabetes, Osteoporosis, CHD, Schizophrenia, etc.)
7. Pharmacogenetics studies on HSD inhibitor development programs
2005 - 2007
Scientist, Affymetrix, Inc.
Projects: 1. Design of microarray for high throughput genotyping and genome
wide association study (Affymetrix SNP 500K, 5.0 and 6.0)
2. Algorithm in GWAS, arrayCGH and LOH studies
2003-2005
Postdoctoral Research Fellow; Advisor: Wing H. Wong, PhD
Department of Biostatistics, Harvard University
Projects: 1. Linkage mapping for human diseases
2. Transcriptional microarray in characterizing survival and recurrence
of ovarian cancer
3. Methods development and analyses of microarray data
4. Haplotype and LD analyses of human genome
1998-2003
Graduate Student
Program for Population Genetics, Harvard University
Projects: 1. Positional candidate gene approaches in asthma
2. Candidate gene study of preterm delivery
3. Pharmacogenetics study of anti-hypertensive therapy
Selected Publications
1. Hao K, Wang X, Niu T, Xu X, Li A, Chang W, Wang L, Li G, Laird N, Xu X. A candidate gene
association study on preterm delivery: application of high-throughput genotyping technology and advanced
statistical methods. Hum Mol Genet. 2004 Apr 1;13(7):683-91.
2. Hao K, Peng S, Xing H, Yu Y, Huang A, Hong X, Wang Y, Chen C, Wang B, Zhang X, Liu J, Zhu G,
Huo Y, Chen D, Zhao X, Ronnenberg A, Wu D, Niu T, Xu X. 3 Adrenergic receptor polymorphism and
obesity-related phenotypes in hypertensive patients. Obes Res. 2004 Jan;12(1):125-30.
3. Hao K, Xu X, Laird N, Wang X, Xu X. Power estimation of multiple SNP association test of case-control
study and application. Genet Epidemiol. 2004 Jan; 26(1):22-30.
4. Hao K, Niu T, Sangokoya C, Li J, Xu X. SNPkit: an efficient approach to systematic evaluation of
candidate single nucleotide polymorphisms in public databases. Biotechniques. 2002 Oct; 33(4):822-8.
5. Li D, Xing H, Hao K, Peng S, Wu D, Guang W, Huang A, Wang Y, Zhang Y, Yu Y, Li J, Chen C, Wang
B, Zhu G, Huo Y, Chen D, Ronnenberg A, Niu T, Xu X; Hypertensive patients from two rural Chinese
counties respond differently to benezapril: Anhui hypertension health care study; Annals of Epidemiology,
2004, Feb; 14(2):123-8
6. Hao K, Li C, Rosenow C, Wong W; Estimation of genotype error rate using samples with pedigree
information – an application on GeneChip® Mapping 10K array; Genomics. 2004 Oct; 84(4): 623-30
7. Hao K, Li C, Rosenow C, Wong W; Detect and adjust for population stratification in population-based
association study using genomic control markers -- an application of Affymetrix Genechip® Human
Mapping 10K array; European Journal of Human Genetics, 2004 Dec;12(12):1001-6.
8. Huang G, Xing H, Hao K, Peng S, Wu D, Guang W, Huang A, Wang Y, Zhang Y, Yu Y, Li J, Chen C,
Wang B, Zhu G, Huo Y, Chen D, Ronnenberg A, Niu T, Xu X; β2 Adrenergic receptor Arg16Gly
polymorphism and therapeutic effect of benazepril on essential hypertension in two Chinese populations,
Clinical and Experimental Hypertension, 2004 Aug; 26(6): 581- 92
9. Hao K, Peng S, Huang A, Hong X, Zhang Y, Zhao X, Xing H, Li J, Ronnenberg A, Xu X, Niu T, Xu X;
Electrocardiographic left ventricular hypertrophy, β3 adrenergic receptor polymorphism and endpoint of
ACEI treatment of hypertension; Journal of applied research in clinical and experimental therapeutics, 2004,
4(2): 293-301
10. Hao K and Wang X, Incorporating individual error rate into association test of unmatched case-control
design; Human Heredity, 2004;58(3-4):154-63.
11. Hao K, Chen C, Wang B, Yang J, Fang Z, Xu X; Familial aggregation of airway responsiveness -- a
community-based study; Annals of Epidemiology, 2005 Nov;15(10):737-43.
12. Leykin I, Hao K, Meyer N, Cheng J, Pollak M, Smith R, Wong W, Rosenow C, Li C; dChipLinkage:
parametric linkage analysis and visualization of high-density oligonucleotide SNP Array Data. BMC
genetics, 2005; Feb 15;6(1):7.
13. Hao K, Niu T, Xu X, Fang Z, Xu X; Single nucleotide polymorphisms of the KCNS3 gene are
significantly associated with airway hyperresponsiveness; Human Genetics, 2005 Apr;116(5):378-83.
14. Hao K, Liu S, Niu T; A sparse marker extension tree algorithm for selecting the best set of haplotype
tagging single nucleotide polymorphisms, Genet Epidemiol. 2005 Dec; 29(4):336-52
15. Dahia P, Hao K, Rogus J, Colin C, Ross K, Magoffin D, Hayashida C, Aronin N, Cascon A, Armelin A,
Toledo S, Li C, Stiles C. Integrated linkage analysis, genome-wide loss of heterozygosity mapping and
transcription profiling reveal a novel susceptibility locus for pheochromocytoma; Cancer Res. 2005 Nov
1;65(21):9651-8.
16. Beroukhim R, Lin M, Park Y, Hao K, Zhao X, Garraway LA, Fox EA, Hochberg EP, Mellinghoff IK,
Hofer MD, Descazeaud A, Rubin MA, Meyerson M, Wong WH, Sellers WR, Li C. Inferring loss-ofheterozygosity from unpaired tumors using high-density oligonucleotide SNP arrays. PLoS Comput Biol.
2006 May; 2(5):e41
17. Peng S, Yu Y, Hao K, Xing H, Li D, Chen C, Huang A, Hong X, Feng Y, Zhang Y, Li J, Wang B, Wu
D, Wang X, Xu X. Heart rate-corrected QT interval duration is significantly associated with blood pressure
in Chinese hypertensives. J Electrocardiol. 2006 Apr; 39(2):206-10.
18. Wamunyokoli FW, Bonome T, Lee JY, Feltmate CM, Welch WR, Radonovich M, Pise-Masison C,
Brady J, Hao K, Berkowitz RS, Mok S, Birrer MJ. Expression profiling of mucinous tumors of the ovary
identifies genes of clinicopathologic importance. Clin Cancer Res. 2006 Feb 1; 12(3 Pt 1):690-700.
19. Bonome T, Lee JY, Park DC, Radonovich M, Pise-Masison C, Brady J, Gardner GJ, Hao K, Wong WH,
Barrett JC, Lu KH, Sood AK, Gershenson DM, Mok SC, Birrer MJ; Expression profiling of serous low
malignant potential, low-grade, and high-grade tumors of the ovary; Cancer Res. 2005 Nov 15;
65(22):10602-12
20. Feltmate CM, Lee KR, Johnson M, Schorge JO, Wong KK, Hao K, Welch WR, Bell DA, Berkowitz RS,
Mok SC.; Whole-genome allelotyping identified distinct loss-of-heterozygosity patterns in mucinous ovarian
and appendiceal carcinomas. Clin Cancer Res. 2005 Nov 1; 11(21):7651-7.
21. Hao K, Di X, Cawley S, LdCompare: rapid computation of single- and multiple-marker r2 and genetic
coverage. Bioinformatics. 2007 Jan 15;23(2):252-4. Epub 2006 Dec 5.
22. Hao K and Cawley S, Differential dropout among SNP genotypes and impacts on association tests. Hum
Hered. 2007;63(3-4):219-28. Epub 2007 Mar 7.
23. Birrer MJ, Johnson ME, Hao K, Wong KK, Park DC, Bell A, Welch WR, Berkowitz RS,
Mok SC. Whole genome oligonucleotide-based array comparative genomic hybridization analysis identified
fibroblast growth factor 1 as a prognostic marker for advanced-stage serous ovarian adenocarcinomas. J Clin
Oncol. 2007 Jun 1;25(16):2281-7.
24. Hao K, Genome-wide selection of tag SNPs using multiple-marker correlation; Bioinformatics. 2007
Dec 1;23(23):3178-84. Epub 2007 Nov 15.
25. Stany MP, Bonome T, Wamunyokoli F, Zorn K, Ozbun L, Park DC, Hao K, Boyd J, Sood AK,
Gershenson DM, Berkowitz RS, Mok SC, Birrer MJ. Classification of ovarian cancer: a genomic analysis.
Adv Exp Med Biol. 2008; 622:23-33.
26. Schadt EE, Molony C, Chudin E, Hao K, Yang X, Lum PY, Kasarskis A, Zhang B, Wang S, Suver C,
Zhu J, Millstein J, Sieberts S, Lamb J, GuhaThakurta D, Derry J, Storey JD, Avila-Campillo I, Kruger MJ,
Johnson JM, Rohl CA, van Nas A, Mehrabian M, Drake TA, Lusis AJ, Smith RC, Guengerich FP, Strom SC,
Schuetz E, Rushmore TH, Ulrich R. Mapping the genetic architecture of gene expression in human liver.
PLoS Biol. 2008 May 6;6(5):e107.
27. Hao K, Schadt EE, Storey JD, Calibrating the performance of SNP arrays for whole-genome association
studies. PLoS Genet. 2008 Jun 27;4(6):e1000109.
28. Hao K, Luk JM, Lee N, Mao M, Zhang C, Ferguson MD, Lamb J, Dai H, Ng IO, Sham PC, Poon R.
Predicting Prognostics in Hepatocellular Carcinoma after Curative Surgery with Common Clinicopathologic
Parameters. BMC Cancer. 2009 Nov 3;9:389.
29. Hao K, Chudin E, McElwee J, Schadt EE, Accuracy of Genome-Wide Imputation of Untyped Markers
and Impacts on Statistical Power for Association Studies. BMC Genetics, 2009, Jun 16;10:27.
30. Mok SC, Bonome T, Vathipadiekal V, Bell A, Johnson ME, Wong KK, Park DC, Hao K, Yip DK,
Donninger H, Ozbun L, Samimi G, Brady J, Randonovich M, Pise-Masison CA, Barrett JC, Wong WH,
Welch WR, Berkowitz RS, Birrer MJ. A gene signature predictive for outcome in advanced ovarian cancer
identifies a survival factor: microfibril-associated glycoprotein 2. Cancer Cell. 2009 Dec 8;16(6):521-32.
31. Hao K and Kasarskis A, Empirical Data Indicates a Primarily Additive Genetic Model for Expressional
QTLs. iCBBE 2010 IEEE CFP1029C-CDR, ISBN: 978-1-4244-4713-8
32. Hao K, Chudin E, Greenawalt D, Schadt EE. Magnitude of stratification in human populations and
impacts on genome wide association studies. PLoS One. 2010 Jan 13;5(1):e8695.
33. Yang X, Zhang B, Molony C, Chudin E, Hao K, Zhu J, Gaedigk A, Suver C, Zhong H, Leeder
JS, Guengerich FP, Strom SC, Schuetz E, Rushmore TH, Ulrich RG,Slatter JG, Schadt EE, Kasarskis
A, Lum PY. Systematic genetic and genomic analysis of cytochrome P450 enzyme activities in human liver.
Genome Res. 2010 Aug;20(8):1020-36. Epub 2010 Jun 10.
34. Zhang ZJ, Hao K, Shi R, Zhao G, Jiang GX, Song Y, Xu X, Ma J. GSTM1 and GSTT1 null
polymorphisms, smoking and their interaction on oral cancer: a HuGE review and meta-analysis. Am. J.
Epidemiology. 2011 Apr 15;173(8):847-57. Epub 2011 Mar 24.
35. Lamb JR, Zhang C, Xie T, Wang K, Zhang B, Hao K, Chudin E, Fraser HB, Millstein J, Ferguson M,
Suver C, Ivanovska I, Scott M, Philippar U, Bansal D, Zhang Z, Burchard J, Smith R, Greenawalt D, Cleary
M, Derry J, Loboda A, Watters J, Poon RT, Fan ST, Yeung C, Lee NP, Guinney J, Molony C, Emilsson V,
Buser-Doepner C, Zhu J, Friend S, Mao M, Shaw PM, Dai H, Luk JM, Schadt EE. Predictive genes in
adjacent normal tissue are preferentially altered by sCNV during tumorigenesis in liver cancer and may rate
limiting. PLoS One. 2011;6(7):e20090. Epub 2011 Jul 5.
36. Hao K, Lamb J, Zhang C, Xie T, Wang K, Zhang B, Chudin, Lee N, Mao M, Zhong H, Ferguson M, Ng
I, Sham P, Poon P, Molony C, Schadt EE, Dai H and Luk JM. Clinicopathological and Gene Expression
Parameters Predicts Liver Cancer Prognosis, BMC Cancer, 2011 Nov 9;11:481.
37. Woo S, Schadt EE and Hao K. Bayesian method to predict individual SNP genotypes from gene
expression data. Nat Genet. 2012;44(5):603-8.
38. Kreimer A, Litvin O, Hao K, Molony C, Pe'er D, Pe'er I. Inference of modules associated to eQTLs.
Nucleic Acids Res. 2012 Jul 1;40(13):e98. Epub 2012 Mar 24.
39. Hao K, Bossé Y, Nickle DC, Paré PD, Postma DS, Laviolette M, Sandford A, Hackett TL, Daley D,
Hogg JC, Elliott WM, Couture C, Lamontagne M, Brandsma C, van den Berge M, Koppelman G, Reicin AS,
Nicholson DW, Malkov V, Derry JM, Suver C, Tsou JA, Kulkarni A, Zhang C, Vessey R, Opiteck GJ,
Curtis SP, Timens W, Sin DD. Lung eQTLs to Help Reveal the Molecular Underpinnings of Asthma, PLoS
Genetics, in press
Lecture and Oral Presentations
Bioconductor Workshop
2006, Seattle WA
Title: rapid computation of single- and multiple-marker r2 and genetic coverage
American Society of Human Genetics
2008 Philadelphia PA
Title: accuracy of genome-wide imputation of untyped markers and impacts on
statistical power for association studies
The West Lake Conference
2009, Hangzhou, China
Title: magnitude of stratification in human populations and impacts on genome wide
association studies.
International Conference on Bioinformatics and Biomedical Engineering, 2010
Title: empirical data indicates a primarily additive genetic model for eQTLs
Published Software
SNPkit, implemented in PERL, designs mutagenic PCR-RFLP assays for
SNP evaluation and genotyping.
MinP, implemented in C++, conducts multiple SNP association tests and
provides global p-values.
GERE (Genotyping Error Rate Estimator), implemented in PERL/TK,
estimates genotyping error rate in pedigree data.
LdCompare, implemented in C++, compute single- and multi- marker r2 at
a genome wide scale.
MultiTag, implemented in C++, Genome-wide selection of tag SNPs using
multiple-marker correlation