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Your Environment. Your Health.

Min Shi, M.D., Ph.D.

Biostatistics Branch

Min Shi, M.D., Ph.D.
Min Shi, M.D., Ph.D.
Staff Scientist
Tel (919) 541-3256
Fax (919) 541-4311
shi2@niehs.nih.gov
P.O. Box 12233
Mail Drop A3-03
Research Triangle Park, North Carolina 27709
Delivery Instructions

Research Summary

Min Shi, M.D., Ph.D., is a staff scientist who develops and applies statistical methods for genetic studies of complex traits. Her research interests include both methodological and applied work, and the interaction between these two areas has inspired many of her research interests.

 

Her methodological research is currently focused on the following topics:

 

  • Family-based and population-based studies
  • Methods for different study designs, such as case-mother/control-mother, case-parents/population-control hybrid and tetrad designs
  • Genome-wide association studies
  • Association studies using data collected from multiple markers
  • Association study with missing data (missing genotypes or missing individuals)
  • Gene-environment, gene-gene interaction and pathway-based analysis
  • Maternally-mediated genetic effects and imprinting effects
  • Copy number variants and rare variants

 

Shi collaborates with investigators in several research projects that include orofacial clefts, prematurity, breast cancer, and asthma. She is currently collaborating with Clarice Weinberg, Ph.D., and David Umbach, Ph.D., in developing statistical methods to analyze genetic data that will be available from the Two Sister Study, a study of young-onset breast cancer. Genetic data will be available for the affected sister and her parents and data on environmental exposure will be collected from the sister pairs. This design (tetrad design) allows for powerful investigation of disease-susceptibility genes as well as maternal and imprinting effects. The gathered environmental data also allows for study of environment effects and gene-by-environment interaction.

Software

  • Case Control
    ("/Rhythmyx/assembler/render?sys_contentid=56407&sys_revision=1&sys_variantid=639&sys_context=0&sys_authtype=0&sys_siteid=&sys_folderid=" sys_dependentvariantid="639" sys_dependentid="56407" inlinetype="rxhyperlink" rxinlineslot="103" sys_dependentid="56407" sys_siteid="" sys_folderid="")This archive provides information for fitting log-linear models and carrying out statistical tests for a design that includes two samples from the same population: one sample of affected individuals and their mothers and a second sample of unaffected individuals and their mothers.
  • Ctrl-mom-hybrid
    ("/Rhythmyx/assembler/render?sys_contentid=56408&sys_revision=1&sys_variantid=639&sys_context=0&sys_authtype=0&sys_siteid=&sys_folderid=" sys_dependentvariantid="639" sys_dependentid="56408" inlinetype="rxhyperlink" rxinlineslot="103" sys_dependentid="56408" sys_siteid="" sys_folderid="")This archive provides information for fitting log-linear models and carrying out statistical tests for a hybrid design that includes a sample of affected individuals and their parents and a sample of unaffected individuals and their mothers (case-parent triad/control-mother dyad design).
  • GEI-TRIMM
    ("/Rhythmyx/assembler/render?sys_contentid=56417&sys_revision=1&sys_variantid=639&sys_context=0&sys_authtype=0&sys_siteid=&sys_folderid=" sys_dependentvariantid="639" sys_dependentid="56417" inlinetype="rxhyperlink" rxinlineslot="103" sys_dependentid="56417" sys_siteid="" sys_folderid="")This package includes the program GEI-TRIMM, which implements the method described in the manuscript Shi M, Umbach DM, Weinberg CR 2010 "Testing Haplotype-Environment Interactions Using Case-parent Triads."
  • LEM scripts
    ("/Rhythmyx/assembler/render?sys_contentid=56421&sys_revision=1&sys_variantid=639&sys_context=0&sys_authtype=0&sys_siteid=&sys_folderid=" sys_dependentvariantid="639" sys_dependentid="56421" inlinetype="rxhyperlink" rxinlineslot="103" sys_dependentid="56421" sys_siteid="" sys_folderid="")This archive provides information for fitting log-linear models and carrying out statistical tests for preterm birth study.
  • Lem Scripts Case-Sibling (http://www.niehs.nih.govhttp://edit:9992/Rhythmyx/assembler/render?sys_authtype=0&sys_variantid=567&sys_revision=1&sys_contentid=75459&sys_context=0)
    This package contains R scripts for analyzing case-sibling data using missing-parents approach as described in the manuscript Shi M, Umbach DM, Weinberg CR 2012 "Case-sibling studies that acknowledge unstudied parents and enroll unmatched individuals".
  • R-SCRIPTS
    ("/Rhythmyx/assembler/render?sys_contentid=56430&sys_revision=1&sys_variantid=639&sys_context=0&sys_authtype=0&sys_siteid=&sys_folderid=" sys_dependentvariantid="639" sys_dependentid="56430" inlinetype="rxhyperlink" rxinlineslot="103" sys_dependentid="56430" sys_siteid="" sys_folderid="")This package contains two R scripts for generating scenarios 1-4 described in the manuscript Shi M, Weinberg CR 2011 "How much are we missing in SNP-by-SNP analyses of GWAS?"
  • TRIad Multi-Marker
    ("/Rhythmyx/assembler/render?sys_contentid=35906&sys_revision=3&sys_variantid=639&sys_context=0&sys_authtype=0&sys_siteid=&sys_folderid=" sys_dependentvariantid="639" sys_dependentid="35906" inlinetype="rxhyperlink" rxinlineslot="103" sys_dependentid="35906" sys_siteid="" sys_folderid="")Performs association tests for a child's or mother's genetic effects using multiple markers from triad families.
  • TRIMMEST
    ("/Rhythmyx/assembler/render?sys_contentid=56435&sys_revision=1&sys_variantid=639&sys_context=0&sys_authtype=0&sys_siteid=&sys_folderid=" sys_dependentvariantid="639" sys_dependentid="56435" inlinetype="rxhyperlink" rxinlineslot="103" sys_dependentid="56435" sys_siteid="" sys_folderid="")This package contains programs that fit log-linear models to estimate the relative risk associated with a candidate risk haplotype in a triad-based association study.

Selected Publications

  1. Shi M, Christensen K, Weinberg CR, Romitti P, Bathum L, Lozada A, Morris RW, Lovett M, Murray JC (2007) "Orofacial cleft risk is increased with maternal smoking and specific detoxification-gene variants" Am J Hum Genet 80(1): 76-90[Abstract ]  
  2. Shi M, Umbach DM, Weinberg CR (2007) "Identification of risk-related haplotypes using multiple linked SNPs from nuclear families" Am J Hum Genet 81(1): 53-66[Abstract ]  
  3. Ehn N, Cooper M, Orr K, Shi M, Johnson M, Caprau D, Dagle J, Johnson K, Marazita M, Merrill D, Murray JC (2007) "Evaluation of fetal and maternal genetic variation in the progesterone receptor gene for contributions to preterm birth" Pediatr Res 62(5): 630-634[Abstract ]  
  4. Steffen KM, Cooper ME, Shi Mi, Caprau D, Simhan HC, Dagle J, Marazita ML, Murray JC (2007) "Maternal and fetal variation in genes of cholesterol metabolism is associated with preterm delivery" J Perinatol 27 (11): 672-680[Abstract ]  
  5. Kimani J, Shi M, Daack-Hirsch S, Christensen K, Moretti-Ferreira D, Marazita M, Field L, Canady J, Murray JC (2007) "X-chromosome inactivation patterns in monozygotic twins and sib pairs discordant for non-syndromic cleft lip and/or palate" Am J Med Genet 143A: 3267-72[Abstract ]  
  6. Shi M, Wehby GL, Murray JC (2008) Review on genetic variants and maternal smoking in the etiology of oral clefts and other birth defects. Birth Defects Res C 84(1): 16-29[Abstract ]  
  7. Shi M, Umbach DM, Vermeulen SH, Weinberg CR (2008) "Making the most of case-mother/control-mother studies" Am J Epidemiol 168: 541-47[Abstract ]  
  8. Vermeulen SH, Shi M, Weinberg CR, Umbach DM (2008) "A hybrid design: case-parent triads supplemented by control-mother dyads" Genet Epidemiol 33(2): 136-44[Abstract ]  
  9. Shi M*, Mostowska A*, Jugessur A, Johnson MK, Mansilla A, Christensen K, Lie RT, Wilcox A, Murray JC (2009) "Identification of microdeletions in candidate genes for cleft lip and/or palate" Birth Defects Res Part A Clin Mol Teratol 85:42-51 (*These authors contributed equally to this work)[Abstract ]  
  10. Boyles AL, Wilcox AJ, Taylor JA, Shi M, Weinberg CR, Meyer K, Fredriksen A, Ueland PM, Johansen AMW, Drevon CA, Jugessur A, Trung TN, Gjessing HK, Vollset SE, Murray JC, Christensen K, Lie RT (2009) "Oral facial clefts and gene polymorphisms in metabolism of folate/one-carbon and vitamin A: a pathway-wide association study" Genet Epidemiol 33: 247-255[Abstract ]  
  11. Shi M, Umbach DM, Weinberg CR (2009) "Using case-parent triads to estimate relative risk associated with a candidate haplotype" Annals of Hum Genet 73(pt3): 346-59[Abstract ]  
  12. Kistner E, Shi M, Weinberg CR (2009) "Using cases and parents to study multiplicative gene-by-environment interaction" Am J Epidemiol 170:393-400[Abstract ]  
  13. Jugessur A*, Shi M*, Gjessing HK, Lie RT, Wilcox AJ, Weinberg CR, Christensen K, Boyles A, Daack-Hirsch S, Trung TN, Billie C, Lidral A, Murray JC (2009) "Genetic determinants of facial clefting: analysis of 357 candidate genes using in two national cleft studies from Scandinavia" PLoS ONE 4(4):e5385 (*These authors contributed equally to this work)[Abstract ]
  14. Weinberg CR, Shi M (2009) "The genetics of preterm birth: Using what we know to design better association studies" Am J Epidemiol 170:1373-1381[Abstract ]  
  15. Kimani J, Yoshiura K, Shi M, Jugessur A, Moretti-Ferreira J, Christensen K, Murray JC, (2009) "Search for genomic alterations in monozygotic twins discordant for cleft lip and/or palate" Twin Research and Human Genetics 12(5): 462-468[Abstract ]  
  16. Hancock DB, Romieu I, Shi M, Sienra-Monge J-J, Wu H, Chiu GY, Li H, del Rio-Navarro BE, Willis-Owens SAG, Weiss ST, Raby BA, Gao H, Eng C, Chapela R, Burchard EG, Tang H, Sullivan PF, London SJ (2009) "Genome-wide association study implicates chromosome 9q21.31 as a susceptibility locus for asthma in Mexican children" PLoS Genet 5(8): e1000623.[Abstract ]  
  17. Wu H, Romieu I, Shi M, Hancock DB, Li H, Sienra-Monge JJ, Chiu GY, Xu H, Estela del Rio-Navarro B, London SJ (2010) "Evaluation of candidate genes in a genome-wide association study of childhood asthma in Mexicans" The Journal of Allergy and Clinical Immunology 125(2): 321-327.e13[Abstract ]  
  18. Shi M, Umbach DM, Weinberg CR (2010) "Testing haplotype-environment interactions using case-parent triads" Human Heredity 70: 23-33[Abstract ]  
  19. Jugessur A*, Shi M*, Gjessing HK, Lie RT, Wilcox AJ, Weinberg CR, Christensen K, Boyles AL, Daack-Hirsch S, Nguyen TT, Christiansen L, Lidral AC and Murray JC (2010) "Maternal genes and facial clefts in offspring: A comprehensive search for genetic associations in two population-based cleft studies from Scandinavia" PLoS One 5(7): e11493 (*These authors contributed equally to this work)[Abstract ]  
  20. Jugessur A, Shi M, Gjessing HK, Lie RT, Wilcox AJ, Weinberg CR , Christensen K, Boyles AL, Daack-Hirsch S, Nguyen TT, Christiansen L, Lidral AC and Murray JC (2011) "Fetal genetic risk of isolated cleft lip only versus isolated cleft lip and palate: A subphenotype analysis using two population-based studies of orofacial clefts in scandinavia" Birth Defects Res Part A Clin Mol Teratol 91(2): 85-92[Abstract ]  
  21. Shi M, London SJ, Chiu GY, Hancock DB, Zaykin D, Weinberg CR (2011) "Using imputed genotypes for relative risk estimation in case-parent studies" Am J of Epidem 173(5): 553-559[Abstract ]  
  22. Shi M, Umbach DM, Weinberg CR (2011) Family based Gene-by-Environment Interaction Studies: Revelations and Remedies. Epidemiology (Cambridge, Mass.) 22(3):400-407[Abstract ]
  23. Weinberg, CR, Shi M, Umbach DM (2011) "A sibling-augmented case-only approach for assessing multiplicative gene-environment interactions." American journal of epidemiology  174(10):1183-1189.[Abstract ]
  24. Shi M, Weinberg CR. (2011) "How much are we missing in SNP-by-SNP analyses of genome-wide association studies?" Epidemiology (Cambridge, Mass.) 22(6):845-847.[Abstract ]
  25. Torgerson DG, Ampleford EJ, Chiu GY, Gauderman WJ, Gignoux CR, Graves PE, Himes BE, Levin AM, Matthias RA, Hancock DB, Baurley JW, Eng C, Stern DA, Celedon JC, Rafaels N, Capurso D, Conti DV, Roth LA, Soto-Quiros M, Togias A, LI X, MYERS RA, Romieu I, Van Den Berg DJ, Hu D, Hansel NN, Hernandez RD, Israel E, Salam MT, Galanter J, Avila PC, Avila L, Rodriquez-Santana JR, Chapela R, Rodriguez-Cintron W, Diette GB, Adkinson NF, Abel RA, Ross KD, Shi M, Faruque MU, Dunston GM, Watson HR, Mantese VJ, Liang L, Ruczinski I, Ford JG, Huntsman S, Chung KF, Vora H, Li X, Calhoun WJ, Castro M, Sierra-Monge JJ, del Rio-Navarro B, Deichmann KA, Heinzmann A, Wenzel SE, Busse WW, Gern JE, Lemanske RF Jr, Beaty TH, Bleecker ER, Raby BA, Meyers DA, London SJ. (2011) "Meta-analysis of Genome-wide Association Studies of Asthma in Ethnically Diverse North American Populations." Nature Genetics 43(9):887-892.[Abstract ]
  26. Weinberg CR, Shi M, Umbach DM. (2011) Re.: "Genetic association and gene-environment interaction: a new method for overcoming the lack of exposure information in controls". American journal of epidemiology  173(11):1346-7.[Abstract ]
  27. Wu T, Fallin MD, Shi M, Ruczinski I, Liang KY, Hetmanski JB, Wang H, Ingersoll RG, Huang S, Ye X, Wu-Chou YH, Chen PK, Jabs EW, Shi B, Redett R, Scott AF, Murray JC, Marazita ML, Munger RG, Beaty TH (2012) "Evidence of gene-environment interaction for the RUNX2 gene and environmental tobacco smoke in controlling the risk of cleft lip with/without cleft palate" Birth Defects Res A Clin Mol Teratol 94(2):76-83.[Abstract ]
  28. Shi M, Murray JC, Marazita ML, Munger RG, Ruczinski I, Hetmanski JB, Wu T, Murray T, Redett RJ, Wilcox AJ, Lie RT, Jabs EW, Wu-Chou YH, Chen PK, Wang H, Ye X, Yeow V, Chong SS, Shi B, Christensen K, Scott AF, Patel P, Cheah F, Beaty TH., (2012) "Genome wide study of maternal and parent-of-origin effects on the etiology of orofacial clefts" Am J Med Genet, Part A, 158A(4):784-94.[Abstract ]
  29. van der Zanden LF, Galesloot TE, Feitz WF, Brouwers MM, Shi M, Knoers NV, Franke B, Roeleveld N, van Rooij IA. (2012) Exploration of gene-environment interactions, maternal effects and parent of origin effects in the etiology of hypospadias. The Journal of urology  188(6):2354-60.[Abstract ]
  30. Shi M, Umbach DM, Weinberg CR. Case-sibling studies that acknowledge unstudied parents and enroll unmatched individuals. International journal of epidemiology 42(1):298-307, 2013.[Abstract ]
  31. Weinberg CR, Shi M, DeRoo L, Taylor JA, Sandler DP, Umbach DM (2014) "Asymmetry in family history implicates nonstandard genetic mechanisms: application to the genetics of breast cancer" PLoS Genet 10(3): e1004174.[Abstract ]

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