Professor Andrew Collins BSc (Hons.), MSc, PhD

Professor of Genetic Epidemiology and Bioinformatics

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Professor Andrew Collins is Professor of Genetic Epidemiology and Bioinformatics within Medicine at the University of Southampton.

Professor Collins began his academic career in Southampton in 1989 and was appointed head of the Genetic Epidemiology and Bioinformatics research group in 2002. He has developed diverse research projects spanning non-disjunction and aberrant recombination patterns, bioinformatic prediction of imprinted and disease genes, biological properties of chromosomes, segregation analysis, autozygosity mapping, and linkage mapping studies for various diseases, genome-wide association mapping and next generation sequencing.

He is currently working on the genetic basis of cleft lip and palate, breast cancer and leukemia, along with methodology for analysis of next generation sequencing data and patterns of linkage disequilibrium in human and non-human genomes. Google Scholar:

Qualifications

BSc (Hons.) Zoology, University of Nottingham (1982).
MSc Biological Computation, University of York (1989)
PhD, University of Southampton (1994).

Appointments held

Senior research fellow, Human Genetics, University of Southampton, 1995-1996

Non-clinical lecturer, Human Genetics, University of Southampton,1997-2001

Reader, Human Genetics, University of Southampton, 2001-2005

Research

Responsibilities

Publications

Contact

Research interests

Current research is focused on:

1. The development and application of machine learning methods for the identification of the genetic basis of early onset breast cancer.
2. Development of bioinformatic analyses of next-generation sequencing data and application to cancer genomes.
3. Approaches to meta-analysis to determine the genetic basis of risk and he identification of genetic factors influencing survival in early onset breast cancer.
4. The genetic basis of paediatric inflammatory bowel disease.

Academic unit(s)

Human Development and Health Academic Units

Affiliate academic unit(s)

Human development and physiology Research group

Postgraduate student supervision

2003 Sarah Ennis PhD
2004 William Tapper PhD
2007 Winston Lau PhD
2007 Mikkel Christensen PhD
2008 Tai-Yue Kuo PhD
2008 Jane Gibson PhD
2009 Jay Self DM
2010 Victoria Hammond PhD

Current

Ioannis Politopoulos PhD

University of Southampton

Member of Southampton High Performance Computing steering group.
Member of the Institute for Complex Systems Simulation (ICSS) executive board

Associate Editor for the Annals of Human Genetics and the Open Bioinformatics Journal.

Visiting Professorships, University of Sydney, University of Melbourne.

Articles

Larrayoz, M., Rose-Zerilli, M. J. J., Kadalayil, L., Parker, H., Blakemore, S., Forster, J., ... Strefford, J. C. (2017). Non-coding NOTCH1 mutations in chronic lymphocytic leukemia; their clinical impact in the UK CLL4 trial. Leukemia, 31(2), 510-514. DOI: 10.1038/leu.2016.298

Pengelly, R. J., Vergara Lope, A., Alyousfi, D., Jabalameli, M. R., & Collins, A. (2017). Understanding the disease genome: gene essentiality and the interplay of selection, recombination and mutation. Briefings in Bioinformatics.

Jabalameli, M. R., Briceno, I., Julio, M., Pengelly, R., Ennis, S., & Collins, A. (2016). Aarskog-Scott syndrome: phenotypic and genetic heterogeneity. AIMS Genetics, 3(1), 49-59. DOI: 10.3934/genet.2016.1.49

Pengelly, R., Gheyas, A. A., Kuo, R., Mossotto, E., Seaby, E. G., Burt, D. W., ... Collins, A. (2016). Commercial chicken breeds exhibit highly divergent patterns of linkage disequilibrium. Heredity, 117(5), 375-382. DOI: 10.1038/hdy.2016.47

Pengelly, R., Arias, L., Martinez, J., Upstill-Goddard, R., Seaby, E. G., Gibson, J., ... Briceno, I. (2016). Deleterious coding variants in multi-case families with non-syndromic cleft lip and/or palate phenotypes. Scientific Reports, 6, 30457.

Weston-Bell, N. J., Tapper, W., Gibson, J., Bryant, D., Moreno, Y., John, M., ... Sahota, S. S. (2016). Exome sequencing in classic hairy cell leukaemia reveals widespread variation in acquired somatic mutations between individual tumours apart from the signature BRAF V(600)E lesion. PLoS ONE, 11(2), 1-14. DOI: 10.1371/journal.pone.0149162

Rose-Zerilli, M., Gibson, J., Wang, J., Tapper, W., Davis, Z., Parker, H., ... Strefford, J. (2016). Longitudinal copy number, whole exome and targeted deep sequencing of 'good risk' IGHV-mutated CLL patients with progressive disease. Leukemia, 30(6), 1301-1310. DOI: 10.1038/leu.2016.10

Pengelly, R., Gibson, J., Andreoletti, G., Collins, A., Mattocks, C. J., & Ennis, S. (2015). Erratum to: a SNP profiling panel for sample tracking in whole-exome sequencing studies. Genome Medicine, 7(1), p.44. DOI: 10.1186/s13073-015-0163-1

Kadalayil, L., Rafiq, S., Rose-Zerilli, M. J. J., Pengelly, R. J., Parker, H., Oscier, D., ... Collins, A. (2015). Exome sequence read depth methods for identifying copy number changes. Briefings in Bioinformatics, 16(3), 380-392. DOI: 10.1093/bib/bbu027

Parry, M., Rose-Zerilli, M. J., Ljungstrom, V., Gibson, J., Wang, A., Walewska, R., ... Strefford, J. C. (2015). Genetics and prognostication in splenic marginal zone lymphoma: revelations from deep sequencing. Clinical Cancer Research, 1-25. DOI: 10.1158/1078-0432.CCR-14-2759

Smyth, C., Spakulova, I., Cotton-Barratt, O., Rafiq, S., Tapper, W., Upstill-Goddard, R., ... MacArthur, B. D. (2015). Quantifying the cumulative effect of low-penetrance genetic variants on breast cancer risk. Molecular Genetics & Genomic Medicine, 3(3), 182-188. DOI: 10.1002/mgg3.129

Pengelly, R., Upstill-Goddard, R., Arias, L., Martinez, J., Gibson, J., Knut, M., ... Briceno, I. (2015). Resolving clinical diagnoses for syndromic cleft lip and/or palate phenotypes using whole-exome sequencing. Clinical Genetics, 88(5), 441-449. DOI: 10.1111/cge.12547

Strefford, J., Kadalayil, L., forster, J., Rose-Zerilli, M., Parker, A., Lin, T. T., ... Oscier, D. (2015). Telomere length predicts progression and overall survival in chronic lymphocytic leukemia: data from the UK LRF CLL4 trial. Leukemia, 29, 2411-2414. DOI: 10.1038/leu.2015.217

Pengelly, R., Tapper, W., Gibson, J., Knut, M., Tearle, R., Collins, A., & Ennis, S. (2015). Whole genome sequences are required to fully resolve the linkage disequilibrium structure of human populations. BMC Genomics, 16(1), 666-[10pp]. DOI: 10.1186/s12864-015-1854-0

Miao, X., Rafiq, S., Khan, S., Tapper, W., Collins, A., Upstill-Goddard, R., ... Eccles, D. (2014). A genome wide meta-analysis study for identification of common variation associated with breast cancer prognosis. PLoS ONE, 9(12), e101488-[10pp]. DOI: 10.1371/journal.pone.0101488

Rose-Zerilli, M. J., Forster, J., Parker, H., Parker, A., Rodríguez, A. E., Chaplin, T., ... Strefford, J. C. (2014). ATM mutation rather than BIRC3 deletion and/or mutation predicts reduced survival in 11q-deleted chronic lymphocytic leukemia: data from the UK LRF CLL4 trial. Haematologica, 99(4), 736-742. DOI: 10.3324/haematol.2013.098574

Tapper, W. J., Foulds, N., Cross, N. C. P., Aranaz, P., Score, J., Hidalgo-Curtis, C., ... Collins, A. (2014). Megalencephaly syndromes: exome pipeline strategies for detecting low-level mosaic mutations. PLoS ONE, 9(1), e86940. DOI: 10.1371/journal.pone.0086940

Collins, A. (2014). The genomic and functional characteristics of disease genes. Briefings in Bioinformatics. DOI: 10.1093/bib/bbt091

Pengelly, R., Gibson, J., Andreoletti, G., Collins, A., Mattocks, C. J., & Ennis, S. (2013). A SNP profiling panel for sample tracking in whole-exome sequencing studies. Genome Medicine, 5(9), 89.

Weston-Bell, N., Gibson, J., John, M., Ennis, S., Pfeifer, S., Cezard, T., ... Sahota, S. S. (2013). Exome sequencing in tracking clonal evolution in multiple myeloma following therapy. Leukemia, 27(5), 1188-1191. DOI: 10.1038/leu.2012.287

Gibson, J., Tapper, W., Ennis, S., & Collins, A. (2013). Exome-based linkage disequilibrium maps of individual genes: functional clustering and relationship to disease. Human Genetics, 132(2), 233-243. DOI: 10.1007/s00439-012-1243-6

Rafiq, S., Tapper, W., Collins, A., Khan, S., Politopoulos, I., Gerty, S., ... Eccles, D. (2013). Identification of inherited genetic variations influencing prognosis in early-onset breast cancer. Cancer Research, 73(6), 1883-1891. DOI: 10.1158/0008-5472.CAN-12-3377

Christodoulou, K., Wiskin, A. E., Gibson, J., Tapper, W., Willis, C., Afzal, N. A., ... Ennis, S. (2013). Next generation exome sequencing of paediatric inflammatory bowel disease patients identifies rare and novel variants in candidate genes. Gut, 62(7), 977-984. DOI: 10.1136/gutjnl-2011-301833

Upstill-Goddard, R., Eccles, D., Ennis, S., Rafiq, S., Tapper, W., Fliege, J., & Collins, A. (2013). Support vector machine classifier for estrogen receptor positive and negative early-onset breast cancer. PLoS ONE, 8(7), e68606. DOI: 10.1371/journal.pone.0068606

Oscier, D. G., Rose-Zerilli, M. J. J., Winkelmann, N., de Castro, D. G., Gomez, B., Forster, J., ... Strefford, J. C. (2013). The clinical significance of NOTCH1 and SF3B1 mutations in the UK LRF CLL4 trial. Blood, 121(3), 468-475. DOI: 10.1182/blood-2012-05-429282

Collins, A., Arias, L., Pengelly, R., Martinez, I., & Ennis, S. (2013). The potential for next generation sequencing to characterise the genetic variation underlying nonsyndromic cleft lip and palate phenotypes. OA Genetics, 1(1), 1-6.

Parry, M., Rose-Zerilli, M. J. J., Gibson, J., Ennis, S., Walewska, R., Forster, J., ... Strefford, J. C. (2013). Whole exome sequencing identifies novel recurrently mutated genes in patients with splenic marginal zone lymphoma. PLoS ONE, 8(12), e83244. DOI: 10.1371/journal.pone.0083244

Upstill-Goddard, R., Eccles, D., Fliege, J., & Collins, A. (2012). Machine learning approaches for the discovery of gene-gene interactions in disease data. Briefings in Bioinformatics.

Collins, A., & Ke, X. (2012). Primer1: Primer design Web service for Tetra-Primer ARMS-PCR. The Open Bioinformatics Journal, 6, 55-58. DOI: 10.2174/1875036201206010055

Gibson, J., Hakobyan, S., Cree, A. J., Collins, A., Harris, C. L., Ennis, S., ... Lotery, A. J. (2012). Variation in complement component C1 inhibitor in age-related macular degeneration. Immunobiology, 217(2), 251-255. DOI: 10.1016/j.imbio.2011.07.015

Parker, H., Rose-Zerilli, M. J. J., Parker, A., Chaplin, T., Wade, R., Gardiner, A., ... Strefford, J. C. (2011). 13q deletion anatomy and disease progression in patients with chronic lymphocytic leukemia. Leukemia, 25(3), 489-497. DOI: 10.1038/leu.2010.288

Politopoulos, I., Gibson, J., Tapper, W., Ennis, S., Eccles, D., & Collins, A. (2011). Composite likelihood-based meta-analysis of breast cancer association studies. Journal of Human Genetics, 56(5), 377-382. DOI: 10.1038/jhg.2011.23

Politopoulos, I., Gibson, J., Tapper, W., Ennis, S., Eccles, D., & Collins, A. (2011). Genome-wide association of breast cancer: composite likelihood with imputed genotypes. European Journal of Human Genetics, 19(2), 194-199. DOI: 10.1038/ejhg.2010.157

Gibson, J., Griffiths, H., Collins, A., Yates, J. R. W., Folk, J. C., East, J. S., ... Ennis, S. (2011). Letter to the editor: Genetic variants within chromosome 4q28.3 are not reproducibly associated with age-related macular degeneration (AMD). Acta Ophthalmologica, 89(7), e603-e604. DOI: 10.1111/j.1755-3768.2010.01986.x

Gibson, J., Cree, A., Collins, A., Lotery, A., & Ennis, S. (2010). Determination of a gene and environment risk model for age-related macular degeneration. British Journal of Ophthalmology, 94(10), 1382-1387. DOI: 10.1136/bjo.2010.182568

Ennis, S., Gibson, J., Cree, A. J., Collins, A., & Lotery, A. J. (2010). Support for the involvement of complement factor I in age-related macular degeneration. European Journal of Human Genetics, 18(1), 15-16. DOI: 10.1038/ejhg.2009.113

Chase, A., Ernst, T., Fiebig, A., Collins, A., Grand, F., Erben, P., ... Cross, N. C. P. (2010). TFG, a target of chromosome translocations in lymphoma and soft tissue tumors, fuses to GPR128 in healthy individuals. Haematologica, 95(1), 20-26. DOI: 10.3324/haematol.2009.011536

Borzani, I., Tola, M. R., Caniatti, L., Collins, A., De Santis, G., Luiselli, D., ... Scapoli, C. (2010). The interleukin-1 cluster gene region is associated with multiple sclerosis in an Italian Caucasian population. European Journal of Neurology, 17(7), 930-938. DOI: 10.1111/j.1468-1331.2010.02952.x

Collins, A. (2009). Allelic association: linkage disequilibrium structure and gene mapping. Molecular Biotechnology, 41(1), 83-89. DOI: 10.1007/s12033-008-9110-3

Collins, A. (2009). Approaches to the identification of susceptibility genes. Parasite Immunology, 31(5), 225-233. DOI: 10.1111/j.1365-3024.2008.01089.x

Sabatti, C., Service, S. K., Hartikainen, A-L., Pouta, A., Ripatti, S., Brodsky, J., ... Peltonen, L. (2009). Genome-wide association analysis of metabolic traits in a birth cohort from a founder population. Nature Genetics, 41(1), 35-46. DOI: 10.1038/ng.271

Jones, A. V., Chase, A., Silver, R. T., Oscier, D., Zoi, K., Wang, Y. L., ... Cross, N. C. P. (2009). JAK2 haplotype is a major risk factor for the development of myeloproliferative neoplasms. Nature Genetics, 41(4), 446-449. DOI: 10.1038/ng.334

Gilbert, R. D., Turner, C. L. S., Gibson, J., Bass, P. S., Haq, M. R., Cross, E., ... Robinson, D. O. (2009). Mutations in phospholipase C epsilon 1 are not sufficient to cause diffuse mesangial sclerosis. Kidney International, 75(4), 415-419. DOI: 10.1038/ki.2008.573

Tapper, W., Gibson, J., Morton, N. E., & Collins, A. (2008). A comparison of methods to detect recombination hotspots. Human Heredity, 66(3), 157-169. DOI: 10.1159/000126050

Gibson, J., Tapper, W., Cox, D., Zhang, W., Pfeufer, A., Gieger, C., ... Morton, N. (2008). A multimetric approach to analysis of genome-wide association by single markers and composite likelihood. Proceedings of the National Academy of Sciences of the United States of America, 105(7), 2592-2597. DOI: 10.1073/pnas.0711903105

Ennis, S., Jomary, C., Mullins, R., Cree, A., Chen, X., Macleod, A., ... Lotery, A. (2008). Association between the SERPING1 gene and age-related macular degeneration: a two-stage case-control study. Lancet, 372(9652), 1828-1834. DOI: 10.1016/S0140-6736(08)61348-3

Collins, A., & Lau, W. (2008). CHROMSCAN: genome-wide association using a linkage disequilibrium map. Journal of Human Genetics, 53(2), 121-126. DOI: 10.1007/s10038-007-0226-2

Khatkar, M. S., Nicholas, M. S., Collins, A. R., Zenger, K. R., Cavanagh, J. A. L., Barris, W., ... Raadsma, H. W. (2008). Extent of genome-wide linkage disequilibrium in Australian Holstein-Friesian cattle based on a high-density SNP panel. BMC Genomics, 9(187). DOI: 10.1186/1471-2164-9-187

Gibson, J., Collins, A., & Morton, N. (2008). Individual disease risk and multimetric analysis of Crohn disease. Proceedings of the National Academy of Sciences of the United States of America, 105(41), 15843-15847. DOI: 10.1073/pnas.0808009105

Jakkula, E., Rehnstrom, K., Varilo, T., Pietiläinen, O. P. H., Paunio, T., Pedersen, N. L., ... Peltonen, L. (2008). The genome-wide patterns of variation expose significant substructure in a founder population. American Journal of Human Genetics, 83(6), 787-794. DOI: 10.1016/j.ajhg.2008.11.005

Tapper, W., Hammond, V., Gerty, S., Ennis, S., Simmonds, P., Collins, A., ... Posh Steering Group (2008). The influence of genetic variation in thirty selected genes on the clinical characteristics of early onset breast cancer. Breast Cancer Research, 10(6), R108. DOI: 10.1186/bcr2213

Liao, W., Collins, A., Hobbs, M., Khatkar, M. S., Luo, J., & Nicholas, F. W. (2007). A comparative location database (CompLDB): map integration within and between species. Mammalian Genome, 18(5), 287-299. DOI: 10.1007/s00335-007-9020-x

Maniatis, N., Collins, A., & Morton, N. E. (2007). Effects of single SNPs, haplotypes, and whole-genome LD maps on accuracy of association mapping. Genetic Epidemiology, 31(3), 179-188. DOI: 10.1002/gepi.20199

Lau, W., Kuo, T-Y., Tapper, W., Cox, S., & Collins, A. (2007). Exploiting large scale computing to construct high resolution linkage disequilibrium maps of the human genome. BMC Bioinformatics, 23(4), 517-519. DOI: 10.1093/bioinformatics/btl615

Ennis, S., Goverdhan, S., Cree, A., Hoh, J., Collins, A., & Lotery, A. (2007). Fine-scale linkage disequilibrium mapping of age-related macular degeneration in the complement factor H gene region. British Journal of Ophthalmology, 91(7), 966-970. DOI: 10.1136/bjo.2007.114090

Morton, N., Maniatis, N., Zhang, W., Ennis, S., & Collins, A. (2007). Genome scanning by composite likelihood. American Journal of Human Genetics, 80(1), 19-28. DOI: 10.1086/510401

Zhang, W., Jia, W., Hu, C., Maniatis, N., Collins, A., & Morton, N. E. (2007). Genome-wide association mapping under the Malecot model and composite likelihood. Genetic Epidemiology, 31(5), p.455. DOI: 10.1002/gepi.20247

Tapper, W., Collins, A., & Morton, N. E. (2007). Mapping a gene for rheumatoid arthritis on chromosome 18q21. BMC Proceedings, 1(Suppl 1), p.S18.

Bugge, M., Collins, A., Hertz, J. M., Eiberg, H., Lundsteen, C., Brandt, C. A., ... Petersen, M. B. (2007). Non-disjunction of chromosome 13. Human Molecular Genetics, 16(16), 2004-2010. DOI: 10.1093/hmg/ddm148

Abdollahi, M. R., Lewis, R. M., Gaunt, T. R., Cumming, D. V. E., Rodriguez, S., Rose-Zerilli, M., ... Day, I. N. M. (2007). Quantitated transcript haplotypes (QTH) of AGTR1, reduced abundance of mRNA haplotypes containing 1166C (rs5186:A>C), and relevance to metabolic syndrome traits. Human Mutation, 28(4), 365-373. DOI: 10.1002/humu.20454

Pereira, L. H. M., Pineda, M. A., Rowe, W. H., Fonseca, L. R., Greene, M. H., Offit, K., ... Struewing, J. P. (2007). The BRCA1 Ashkenazi founder mutations occur on common haplotypes and are not highly correlated with anonymous single nucleotide polymorphisms likely to be used in genome-wide case-control association studies. BMC Genetics, 8(68). DOI: 10.1186/1471-2156-8-68

Hall, H. E., Chan, E. R., Collins, A., Judis, L., Shirley, S., Surti, U., ... Hassold, T. J. (2007). The origin of trisomy 13. American Journal of Medical Genetics Part A, 143A(19), 2242-2248. DOI: 10.1002/ajmg.a.31913

Khatkar, M. S., Collins, A., Cavanagh, J. A. L., Hawken, R. J., Hobbs, M., Zenger, K. R., ... Raadsma, H. W. (2006). A first-generation metric linkage disequilibrium map of bovine chromosome. Genetics, 174(1), 79-85. DOI: 10.1534/genetics.106.060418

Chen, L., Velasco Mondragon, H. E., Lazcano-Ponce, E., Collins, A., & Shugart, Y. Y. (2006). Effect of the peroxisome proliferators-activated receptor (PPAR) gamma 3 gene on BMI in 1,210 school students from Morelos, Mexico. Pacific Symposium on Biocomputing, 467-477.

Gibson, J., Morton, N. E., & Collins, A. (2006). Extended tracts of homozygosity in outbred human populations. Human Molecular Genetics, 15(5), 789-795. DOI: 10.1093/hmg/ddi493

Self, J. E., Ennis, S., Collins, A., Shawkat, F., Harris, C. M., Mackey, D. A., ... Lotery, A. J. (2006). Fine mapping of the X-linked recessive congenital idiopathic nystagmus locus at Xq24-q26.3. Molecular Vision, 12, 1211-1216.

Service, S., DeYoung, J., Karayiorgou, M., Roos, J. L., Pretorious, H., Bedoya, G., ... Freimer, N. (2006). Letter. Magnitude and distribution of linkage disequilibrium in population isolates and implications for genome-wide association studies. Nature Genetics, 38(5), 556-560. DOI: 10.1038/ng1770

Zhang, W., Maniatis, N., Rodriguez, S., Miller, G. J., Day, I. N. M., Gaunt, T. R., ... Morton, N. E. (2006). Refined association mapping for a quantitative trait: weight in the H19-IGF2-INS-TH region. Annals of Human Genetics, 70(6), 848-856. DOI: 10.1111/j.1469-1809.2006.00290.x

Tapper, W., Collins, A., Gibson, J., Maniatis, N., Ennis, S., & Morton, N. E. (2005). A map of the human genome in linkage disequilibrium units. Proceedings of the National Academy of Sciences of the United States of America, 102(33), 11835-11839. DOI: 10.1073/pnas.0505262102

Jia, W-H., Collins, A., Zeng, Y-X., Feng, B-J., Yu, X. J., Huang, L-X., ... Shugart, Y. Y. (2005). Complex segregation analysis of nasopharyngeal carcinoma in Guangdong, China: evidence for a multifactorial mode of inheritance (complex segregation analysis of NPC in China). European Journal of Human Genetics, 13(2), 248-252. DOI: 10.1038/sj.ejhg.5201305

Gibson, J., Tapper, W., Zhang, W., Morton, N., & Collins, A. (2005). Cosmopolitan linkage disequilibrium maps. Human Genomics, 2(1), 20-27.

Scapoli, C., Trombelli, L., Mamolini, E., & Collins, A. (2005). Linkage disequilibrium analysis of case-control data: an application to generalized aggressive periodontitis. Genes and Immunity, 6(1), 44-52. DOI: 10.1038/sj.gene.6364152

Simpson, A., Maniatis, N., Jury, F., Cakebread, J. A., Lowe, L. A., Holgate, S. T., ... John, S. L. (2005). Polymorphisms in a disintegrin and metalloprotease 33 (ADAM33) predict impaired early-life lung function. American Journal of Respiratory and Critical Care Medicine, 172(1), 55-60. DOI: 10.1164/rccm.200412-1708OC

De La Vega, F. M., Isaac, H., Collins, A., Scafe, C. R., Halldórsson, B. V., Su, X., ... Gilbert, D. A. (2005). The linkage disequilibrium maps of three human chromosomes across four populations reflect their demographic history and a common underlying recombination pattern. Genome Research, 15(4), 454-462. DOI: 10.1101/gr.3241705

Maniatis, N., Morton, N. E., Gibson, J., Xu, C-F., Hosking, L. K., & Collins, A. (2005). The optimal measure of linkage disequilibrium reduces error in association mapping of affection status. Human Molecular Genetics, 14(1), 145-153. DOI: 10.1093/hmg/ddi019

Zhang, W., Collins, A., & Morton, N. E. (2004). Does haplotype diversity predict power for association mapping of disease susceptibility? Human Genetics, 115(2), 157-164. DOI: 10.1007/s00439-004-1122-x

Zhang, W., Collins, A., Gibson, J., Tapper, W. J., Hunt, S., Deloukas, P., ... Morton, N. E. (2004). Impact of population structure, effective bottleneck time, and allele frequency on linkage disequilibrium maps. Proceedings of the National Academy of Sciences of the United States of America, 101(52), 18075-18080. DOI: 10.1073/pnas.0408251102

Simpson, C. L., Hansen, V. K., Sham, P. C., Collins, A., Powell, J. F., & Al-Chalabi, A. (2004). MaGIC: a program to generate targeted marker sets for genome-wide association studies. Biotechniques, 37(6), 996-999.

Collins, A., Lau, W., & De La Vega, F. (2004). Mapping genes for common diseases: the case for genetic (LD) maps. Human Heredity, 58(1), 2-9. DOI: 10.1159/000081451

Ke, X., Hunt, S., Tapper, W., Lawrence, R., Stavrides, G., Ghori, J., ... Deloukas, P. (2004). The impact of SNP density on fine-scale patterns of linkage disequilibrium. Human Molecular Genetics, 13(6), 577-588. DOI: 10.1093/hmg/ddh060

Tapper, W. J., Maniatis, N., Morton, N. E., & Collins, A. (2003). A metric linkage disequilibrium map of a human chromosome. Annals of Human Genetics, 67(6), 487 -494. DOI: 10.1046/j.1469-1809.2003.00050.x

Ke, X., & Collins, A. (2003). CpG islands in human X-inactivation. Annals of Human Genetics, 67(3), 242-249. DOI: 10.1046/j.1469-1809.2003.00038.x

Morgan, A., Zhang, B., Tapper, W., Collins, A., & Ye, S. (2003). Haplotypic analysis of the matrix metalloproteinase-9 gene in relation to coronary artery disease. Atherosclerosis Supplements, 4(2), p.321. DOI: 10.1016/S1567-5688(03)91377-8

Morgan, A. R., Zhang, B., Tapper, W., Collins, A., & Ye, S. (2003). Haplotypic analysis of the MMP-9 gene in relation to coronary artery disease. Journal of Molecular Medicine, 81(5), 321-326. DOI: 10.1007/s00109-003-0441-z

Ye, S., Dunleavey, L., Bannister, W., Day, L. B., Tapper, W., Collins, A. R., ... Simpson, I. (2003). Independent effects of the -219 G>T and ?2/ ?3/ ?4 polymorphisms in the apolipoprotein E gene on coronary artery disease: the Southampton Atherosclerosis Study. European Journal of Human Genetics, 11(6), 437-443. DOI: 10.1038/sj.ejhg.5200983

Lonjou, C., Zhang, W., Collins, A., Tapper, W. J., Elahi, E., Maniatis, N., & Morton, N. E. (2003). Linkage disequilibrium in human populations. Proceedings of the National Academy of Sciences of the United States of America, 100(10), 6069-6074. DOI: 10.1073/pnas.1031521100

Maniatis, N., Collins, A., Gibson, J., Zhang, W., Tapper, W., & Morton, N. E. (2003). Positional cloning by linkage disequilibrium. American Journal of Human Genetics, 73(5), 846-855. DOI: 10.1086/383589

Ennis, S., Collins, A., & Morton, N. E. (2003). SNP-based haplotypes and LD blocks in the fragile X region. Journal of Medical Genetics, 40, p.S15.

Ennis, S., Collins, A., & Morton, N. E. (2003). The use of SNP-based haplotypes and LD blocks to positionally clone modifying determinants of expansion of the Fragile X triplet repeat. American Journal of Human Genetics, 73(5), 377.

Zhang, W., Collins, A., Lonjou, C., & Morton, N. E. (2002). A linkage tournament: affection status, parametric analysis, multivariate traits, and enhancements to variance components and relative pairs. Annals of Human Genetics, 66(1), 87-98. DOI: 10.1017/S0003480001008971

Ke, X., Thomas, N. S., Robinson, D. O., & Collins, A. (2002). A novel approach for identifying candidate imprinted genes through sequence analysis of imprinted and control genes. Human Genetics, 111(6), 511 - 520. DOI: 10.1007/s00439-002-0822-3

Fredell, L., Iselius, L., Collins, A., Hansson, E., Holmner, S., Lundquist, L., ... Nordenskjöld, A. (2002). Complex segregation analysis of hypospadias. Human Genetics, 111(3), 231-234. DOI: 10.1007/s00439-002-0799-y

Peacock, C. S., Sanjeevi, C. B., Shaw, M-A., Collins, A., Campbell, R. D., March, R., ... Blackwell, J. M. (2002). Genetic analysis of multicase families of visceral leishmaniasis in northeastern Brazil: no major role for class II or class III regions of HLA. Genes and Immunity, 3(6), 350-358. DOI: 10.1038/sj.gene.6363852

Howell, W. M., Turner, S. J., Collins, A., Bateman, A. C., & Theaker, J. M. (2002). Influence of TNFalpha and LTalpha single nucleotide polymorphisms on susceptibility to and prognosis in cutaneous malignant melanoma in the British population. European Journal of Immunogenetics, 29(1), 17-23. DOI: 10.1046/j.1365-2370.2002.00269.x

Howell, W. M., Bateman, A. C., Turner, S. J., Collins, A., & Theaker, J. M. (2002). Influence of vascular endothelial growth factor single nucleotide polymorphisms on tumour development in cutaneous malignant melanoma. Genes and Immunity, 3(4), 229-232. DOI: 10.1038/sj.gene.6363851

Zhang, W., Collins, A., Abecasis, G. R., Cardon, L. R., & Morton, N. E. (2002). Mapping quantitative effects of oligogenes by allelic association. Annals of Human Genetics, 66(3), 211-221. DOI: 10.1046/j.1469-1809.2002.00111.x

Zhang, W., Collins, A., Maniatis, N., Tapper, W., & Morton, N. E. (2002). Properties of linkage disequilibrium (LD) maps. Proceedings of the National Academy of Sciences of the United States of America, 99(26), 17004-17007. DOI: 10.1073/pnas.012672899

Tapper, W. J., Ke, X., Morton, N. E., & Collins, A. (2002). Recombination, interference and sequence: comparison of chromosomes 21 and 22. Annals of Human Genetics, 66(1), 75-86. DOI: 10.1017/S0003480001008946

Ke, X., Thomas, N. S., Robinson, D. O., & Collins, A. (2002). The distinguishing sequence characteristics of mouse imprinted genes. Mammalian Genome, 13(11), 639-645. DOI: 10.1007/s00335-002-3038-x

Maniatis, N., Collins, A., Xu, C. F., McCarthy, L. C., Hewett, D. R., Tapper, W., ... Morton, N. E. (2002). The first linkage disequilibrium (LD) maps: delineation of hot and cold blocks by diplotype analysis. Proceedings of the National Academy of Sciences of the United States of America, 99(4), 2228-2233.

Shugart, Y. Y., Feng, B-J., & Collins, A. (2002). The power and statistical behaviour of allele-sharing statistics when applied to models with two disease loci. Journal of Genetics, 81(3), 99-103.

Morton, N. E., & Collins, A. (2002). Toward positional cloning with SNPs. Current Opinion in Molecular Therapeutics, 4(3), 259-264.

Tapper, W. J., Morton, N. E., Dunham, I., Ke, X., & Collins, A. (2001). A sequence-based integrated map of chromosome 22. Genome Research, 11(7), 1290-1295. DOI: 10.1101/gr.161301

Zhang, W., Tapper, W., Collins, A., Jacobs, K. B., Elston, R. C., & Morton, N. E. (2001). A tournament of linkage tests in complex inheritance. Human Heredity, 52(3), 140-148. DOI: 10.1159/000053369

Ennis, S., Maniatis, N., & Collins, A. (2001). Allelic association and disease mapping. Briefings in Bioinformatics, 2(4), 375-387. DOI: 10.1093/bib/2.4.375

Ennis, S., Collins, A., Tapper, W., Murray, A., MacPherson, J. N., & Morton, N. E. (2001). Allelic association discriminates draft orders. Annals of Human Genetics, 65(5), 503-504. DOI: 10.1046/j.1469-1809.2001.6550503.x

Collins, A., Ennis, S., Taillon-Miller, P., Kwok, P-Y., & Morton, N. E. (2001). Allelic association with SNPs: metrics, populations, and the linkage disequilibrium map. [In Special Issue: SNP 2000: Third International Meeting on Single Nucleotide Polymorphism and Complex Genome Analysis]. Human Mutation, 17(4), 255-262. DOI: 10.1002/humu.21

Ye, S., Dhillon, S., Ke, X., Collins, A. R., & Day, I. N. M. (2001). An efficient procedure for genotyping single nucleotide polymorphisms. Nucleic Acids Research, 29(17), p.E88.

Shaw, M-A., Donaldson, I. J., Collins, A., Peacock, C. S., Lins-Lainson, Z., Shaw, J. J., ... Blackwell, J. M. (2001). Association and linkage of leprosy phenotypes with HLA class II and tumour necrosis factor genes. Genes and Immunity, 2(4), 196-204.

Zhang, W., Collins, A., & Morton, N. E. (2001). Combination of linkage evidence in complex inheritance. Human Heredity, 52(3), 132-135. DOI: 10.1159/000053367

Malmer, B., Iselius, L., Holmberg, E., Collins, A., Henriksson, R., & Grönberg, H. (2001). Genetic epidemiology of glioma. British Journal of Cancer, 84(3), 429-434. DOI: 10.1054/bjoc.2000.1612

Peacock, C. S., Collins, A., Shaw, M-A., Silveira, F., Costa, J., Coste, C. H., ... Blackwell, J. M. (2001). Genetic epidemiology of visceral leishmaniasis in northeastern Brazil. Genetic Epidemiology, 20(3), 383-396. DOI: 10.1002/gepi.8

Ennis, S., Collins, A., Murray, A., Brightwell, G., & Morton, N. E. (2001). LD, FRAX and sequence-based maps. American Journal of Human Genetics, 69(4), 466.

Ke, X., Tapper, W., & Collins, A. (2001). LDB2000: sequence-based integrated maps of the human genome. Bioinformatics, 17(7), 581-586.

Thomas, N. S., Ennis, S., Sharp, A. J., Durkie, M., Hassold, T. J., Collins, A. R., & Jacobs, P. A. (2001). Maternal sex chromosome non-disjunction: evidence for X chromosome-specific risk factors. Human Molecular Genetics, 10(3), 243-250. DOI: 10.1093/hmg/10.3.243

Ke, X., Collins, A., & Ye, S. (2001). PIRA PCR designer for restriction analysis of single nucleotide polymorphisms. Bioinformatics, 17(9), 838-839. DOI: 10.1093/bioinformatics/17.9.838

Morton, N. E., Zhang, W., Taillon-Miller, P., Ennis, S., Kwok, P. Y., & Collins, A. (2001). The optimal measure of allelic association. Proceedings of the National Academy of Sciences of the United States of America, 98(9), 5217-5221. DOI: 10.1073/pnas.091062198

Ennis, S., Collins, A., Murray, A., MacPherson, J. N., & Morton, N. E. (2000). Allelic association in the FRAX region. Annals of Human Genetics, 64(6), 513-518. DOI: 10.1046/j.1469-1809.2000.6460513.x

Collins, A., Ennis, S., Tapper, W., & Morton, N. E. (2000). Mapping oligogenes for atopy and asthma by meta-analysis. Genetics and Molecular Biology, 23(1), 1-10. DOI: 10.1590/S1415-47572000000100001

Collins, A., Lonjou, C., & Morton, N. E. (1999). Genetic epidemiology of single-nucleotide polymorphisms. Proceedings of the National Academy of Sciences, 96(26), 15173-15177. DOI: 10.1073/pnas.96.26.15173

Lonjou, C., Collins, A., Ennis, S., Tapper, W., & Morton, N. E. (1999). Meta-analysis and retrospective collaboration: two methods to map oligogenes for atopy and asthma. Clinical & Experimental Allergy, 29, 57-59.

Morton, N. E., & Collins, A. (1998). Tests and estimates of allelic association in complex inheritance. Proceedings of the National Academy of Sciences, 95(19), 11389-11393. DOI: 10.1073/pnas.95.19.11389

Book

Collins, A. R. (Ed.) (2008). Linkage disequilibrium and association mapping: analysis and applications. (Methods in Molecular Biology; Vol. 376). Totowa, USA: Humana. DOI: 10.1007/978-1-59745-389-9

Book Chapters

Collins, A. (2013). Linkage analysis and gene mapping. In M. J. Zvelebil, & J. M. Hancock (Eds.), Concise Encyclopaedia of Bioinformatics and Computational Biology 2nd edition. Hoboken, US: John Wiley & Sons.

Kuo, T-Y., Lau, W., & Collins, A. R. (2008). LDMAP: the construction of high-resolution linkage disequilibrium maps of the human genome. In A. R. Collins (Ed.), Linkage Disequilibrium and Association Mapping: Analysis and Applications. (pp. 47-57). (Methods in Molecular Biology; Vol. 376). Totowa, USA: Humana. DOI: 10.1007/978-1-59745-389-9_4

Collins, A. R. (2008). Linkage disequilibrium and association mapping: an introduction. In A. R. Collins (Ed.), Linkage Disequilibrium and Association Mapping. (pp. 1-15). (Methods in Molecular Biology; Vol. 376). Totowa, USA: Humana. DOI: 10.1007/978-1-59745-389-9_1

Collins, A., & Morton, N. (2007). Genome scanning by composite likelihood. In M. Weale (Ed.), Genetic Epidemiology II: Latest Developments. (The Biomedical & Life Sciences Collection). London, UK: Henry Stewart Talks.

Morton, N., & Collins, A. (2004). Optimal use of linkage disequilibrium, haplotypes, and integrated maps for positional cloning. In M. Weale (Ed.), Genetic Epidemiology I: Fundamentals, Theory, Practice and Latest Developments. (The Biomedical & Life Sciences Collection). London, UK: Henry Stewart Talks.

Collins, A. (2003). Genetics maps: integration. In D. Cooper (Ed.), Nature Encyclopedia of the Human Genome. (pp. 888-891). London, UK: Nature Publishing Group.

Report

Scott, M., Boardman, R. P., Reed, P. A. S., Byatt, D., Stark, I., Cox, S. J., ... Soady, K. A. (2016). Introducing research data - fourth edition. Southampton, GB: University of Southampton.

Professor Andrew Collins
Faculty of Medicine, University of Southampton, Building 85, Life Sciences Building, Highfield Campus, Southampton, SO171BJ

Room Number:SGH/Duthie/MP808

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