Research Topics
Genomes and Genes
Species | Chris Tyler-SmithSummaryAffiliation: Wellcome Trust Genome Campus Country: UK Publications
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Detail Information
Publications
Contrasting signals of positive selection in genes involved in human skin-color variation from tests based on SNP scans and resequencingJohanna Maria de Gruijter
Department of Forensic Molecular Biology, Erasmus MC University Medical Center, PO Box 2040, Rotterdam, 3000 CA, The Netherlands
Investig Genet 2:24. 2011..abstract:..- Comprehensive comparison of three commercial human whole-exome capture platforms- Asan
Beijing Institute of Genomics, Chinese Academy of Sciences, No 7 Beitucheng West Road, Chaoyang District, Beijing 100029, China
Genome Biol 12:R95. 2011..Currently, there are several commercial human exome capture platforms; however, the relative performances of these have not been characterized sufficiently to know which is best for a particular study... - The functional spectrum of low-frequency coding variationGabor T Marth
Department of Biology, Boston College, 140 Commonwealth Avenue, Chestnut Hill, MA 02467, USA
Genome Biol 12:R84. 2011.... - Sibling rivalry among paralogs promotes evolution of the human brainChris Tyler-Smith
The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, UK
Cell 149:737-9. 2012..Two papers in this issue suggest that partial duplication of SRGAP2, producing an incomplete protein that antagonizes the original, contributed to human brain evolution... - Variation of 52 new Y-STR loci in the Y Chromosome Consortium worldwide panel of 76 diverse individualsSi Keun Lim
The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SA, UK
Int J Legal Med 121:124-7. 2007..Ten loci showed occasional missing alleles, duplicated peaks or intermediate-sized alleles... - Genetic variation in Northern Thailand Hill Tribes: origins and relationships with social structure and linguistic differencesDavide Besaggio
Dipartimento di Biologia ed Evoluzione, Universita di Ferrara, Via L, Borsari 46, 44100 Ferrara, Italy
BMC Evol Biol 7:S12. 2007..Using both original and published data on the Hill Tribes and several other Asian populations, we focused on all these aspects... - An evolutionary perspective on Y-chromosomal variation and male infertilityChris Tyler-Smith
The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Cambridgeshire, UK
Int J Androl 31:376-82. 2008.... - Population differentiation as an indicator of recent positive selection in humans: an empirical evaluationYali Xue
The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton CB10 1SA, United Kingdom
Genetics 183:1065-77. 2009.... - A map of human genome variation from population-scale sequencingRichard M Durbin
Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Cambridge CB10 1SA, UK
Nature 467:1061-73. 2010..These methods and public data will support the next phase of human genetic research... - A worldwide survey of human male demographic history based on Y-SNP and Y-STR data from the HGDP-CEPH populationsWentao Shi
The Wellcome Trust Sanger Institute, Hinxton, Cambs, United Kingdom
Mol Biol Evol 27:385-93. 2010..However, some unexpected demographic histories were also found, including low growth rates in the Hazara and Kalash from Pakistan and recent expansion of the Mozabites in North Africa... - Relative impact of nucleotide and copy number variation on gene expression phenotypesBarbara E Stranger
Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SA, UK
Science 315:848-53. 2007..Interrogation of the genome for both types of variants may be an effective way to elucidate the causes of complex phenotypes and disease in humans... - Adaptive evolution of UGT2B17 copy-number variationYali Xue
The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton CB10 1SA, UK
Am J Hum Genet 83:337-46. 2008..In contrast, diversity was low in East Asia where a single haplotype predominated, suggesting positive selection for the deletion in this part of the world... - Exploration of signals of positive selection derived from genotype-based human genome scans using re-sequencing dataMin Hu
The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, CB10 1SA, UK
Hum Genet 131:665-74. 2012.... - High altitude adaptation in Daghestani populations from the CaucasusLuca Pagani
The Wellcome Trust Sanger Institute, Hinxton, UK
Hum Genet 131:423-33. 2012..These variants illustrate both the common pathways of adaptation to high altitude in different populations and features specific to the Daghestani populations, showing how even a mildly hypoxic environment can lead to genetic adaptation... - Origins and functional impact of copy number variation in the human genomeDonald F Conrad
The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SA UK
Nature 464:704-12. 2010.... - Spread of an inactive form of caspase-12 in humans is due to recent positive selectionYali Xue
The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambs CB10 1SA, United Kingdom
Am J Hum Genet 78:659-70. 2006..We further propose that its selective advantage was sepsis resistance in populations that experienced more infectious diseases as population sizes and densities increased... - Global variation in copy number in the human genomeRichard Redon
The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SA, UK
Nature 444:444-54. 2006..The data obtained delineate linkage disequilibrium patterns for many CNVs, and reveal marked variation in copy number among populations. We also demonstrate the utility of this resource for genetic disease studies... 
Genetic variation in South Asia: assessing the influences of geography, language and ethnicity for understanding history and disease riskQasim Ayub
The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, UK
Brief Funct Genomic Proteomic 8:395-404. 2009....- Human Y chromosome base-substitution mutation rate measured by direct sequencing in a deep-rooting pedigreeYali Xue
The Wellcome Trust Sanger Institute, Hinxton, Cambs CB10 1SA, UK
Curr Biol 19:1453-7. 2009..0 x 10(-8)), consistent with estimates of 2.3 x 10(-8)-6.3 x 10(-8) mutations/nucleotide/generation for the same Y-chromosomal region from published human-chimpanzee comparisons depending on the generation and split times assumed... - Variation in genome-wide mutation rates within and between human familiesDonald F Conrad
Wellcome Trust Sanger Institute, Hinxton, Cambridge, UK
Nat Genet 43:712-4. 2011..These observations suggest considerable variation in mutation rates within and between families... - Insights into hominid evolution from the gorilla genome sequenceAylwyn Scally
Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton CB10 1SA, UK
Nature 483:169-75. 2012..The use of the genome sequence in these and future analyses will promote a deeper understanding of great ape biology and evolution... - The hare and the tortoise: one small step for four SNPs, one giant leap for SNP-kindYali Xue
The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambs CB10 1SA, UK
Forensic Sci Int Genet 4:59-61. 2010..Y-SNPs therefore now offer the best resolution of Y haplotypes and promise to distinguish almost every Y chromosome. This work illustrates the promise of current sequencing technology for forensically relevant applications... - A world in a grain of sand: human history from genetic dataVincenza Colonna
The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire, UK
Genome Biol 12:234. 2011..To see a world in a grain of sand ...William Blake, Auguries of Innocence... - A genome-wide survey of the prevalence and evolutionary forces acting on human nonsense SNPsBryndis Yngvadottir
The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambs CB10 1SA, UK
Am J Hum Genet 84:224-34. 2009..This study underlines the extent of variation in gene content within humans and emphasizes the importance of understanding this type of variation... - Geographical affinities of the HapMap samplesMiao He
The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, United Kingdom
PLoS ONE 4:e4684. 2009..What effects could this non-standard ascertainment have on the interpretation of HapMap results?.. - A systematic survey of loss-of-function variants in human protein-coding genesDaniel G MacArthur
Wellcome Trust Sanger Institute, Hinxton, UK
Science 335:823-8. 2012..We describe functional and evolutionary differences between LoF-tolerant and recessive disease genes and a method for using these differences to prioritize candidate genes found in clinical sequencing studies... - Long-range, high-throughput haplotype determination via haplotype-fusion PCR and ligation haplotypingDaniel J Turner
Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Cambridge, UK
Nucleic Acids Res 36:e82. 2008..4 kb apart on chromosome 7, and which influence an individual's susceptibility to systemic lupus erythematosus... - The promise and reality of personal genomicsBryndis Yngvadottir
The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton CB10 1SA, UK
Genome Biol 10:237. 2009..The publication of the highest-quality and best-annotated personal genome yet tells us much about sequencing technology, something about genetic ancestry, but still little of medical relevance... - The functional impact of structural variation in humansMatthew E Hurles
The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SA, UK
Trends Genet 24:238-45. 2008.... - Y-chromosomal insights into the genetic impact of the caste system in IndiaTatiana Zerjal
The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambs, CB10 1SA, UK
Hum Genet 121:137-44. 2007..In the other castes, there may be either larger effective population sizes, or less strict isolation, or both... - A systematic, large-scale resequencing screen of X-chromosome coding exons in mental retardationPatrick S Tarpey
Wellcome Trust Sanger Institute, Hinxton, Cambridge, UK
Nat Genet 41:535-43. 2009..The study has, however, also highlighted issues confronting whole-genome sequencing screens, including the observation that loss of function of 1% or more of X-chromosome genes is compatible with apparently normal existence... - Assaying chromosomal inversions by single-molecule haplotypingDaniel J Turner
Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SA, UK
Nat Methods 3:439-45. 2006..The generality of our methods to survey for, and genotype chromosomal inversions should help our understanding of the contribution of inversions to genomic variation, inherited diseases and cancer... - The variant call format and VCFtoolsPetr Danecek
Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Cambridge CB10 1SA, UK
Bioinformatics 27:2156-8. 2011..VCFtools is a software suite that implements various utilities for processing VCF files, including validation, merging, comparing and also provides a general Perl API. AVAILABILITY: http://vcftools.sourceforge.net.. 
The population history of the Xibe in northern China: a comparison of autosomal, mtDNA and Y-chromosomal analyses of migration and gene flowGareth T Powell
The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire CB10 1SA, UK
Forensic Sci Int Genet 1:115-9. 2007..In the Chinese samples examined, the combination of a northeastern autosomal background with a northwestern Y chromosome is indicative of a Xibe individual...- Recent spread of a Y-chromosomal lineage in northern China and MongoliaYali Xue
The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, United Kingdom
Am J Hum Genet 77:1112-6. 2005..4% of the minority population by the end of the dynasty... - A genome-wide meta-analysis identifies 22 loci associated with eight hematological parameters in the HaemGen consortiumNicole Soranzo
Human Genetics, Wellcome Trust Sanger Institute, Hinxton, UK
Nat Genet 41:1182-90. 2009.... - HI: haplotype improver using paired-end short readsQuan Long
The Wellcome Trust Sanger Institute, Hinxton, Cambs, UK
Bioinformatics 25:2436-7. 2009..We find that given a fixed coverage, longer reads (implying fewer of them) are preferable. AVAILABILITY: The executable and user manual can be freely downloaded from ftp://ftp.sanger.ac.uk/pub/zn1/HI... - Variation of the oxytocin/neurophysin I (OXT) gene in four human populationsYang Xu
The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambs, CB10 1SA, UK
J Hum Genet 53:637-43. 2008.... - The sequences of the human sex chromosomesMark T Ross
Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SA, UK
Curr Opin Genet Dev 16:213-8. 2006..In addition, they have been useful for identifying variants associated with simple Mendelian disorders such as microphthalmia or mental retardation, and more complex disorders such as osteoporosis... - Loss-of-function variants in the genomes of healthy humansDaniel G MacArthur
Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, UK
Hum Mol Genet 19:R125-30. 2010.... - Response to the comment on "The hare and the tortoise: One small step for four SNPs, one giant leap for SNP-kind"Yali Xue
The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambs CB10 1SA, UK
Forensic Sci Int Genet 5:361-2. 2011..However, changes to ethical and legal structures may be needed before the new information could be used... - Ancient Indian roots?Denise R Carvalho-Silva
The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambs, UK
J Biosci 31:1-2. 2006 - Detection of novel Y SNPs provides further insights into Y chromosomal variation in PakistanAisha Mohyuddin
Biomedical and Genetic Engineering Laboratories, G. P. O Box 2891, 44000, Islamabad, Pakistan
J Hum Genet 51:375-8. 2006..BATWING analysis gave an estimate of between 2,500 and 7,300 YBP for population expansion in Pakistan which coincides with the period of the Indus Valley civilizations... - A comprehensive survey of human Y-chromosomal microsatellitesManfred Kayser
Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
Am J Hum Genet 74:1183-97. 2004..As a result of this work, a large number of new, highly polymorphic Y-chromosomal microsatellites are now available for population-genetic, evolutionary, genealogical, and forensic investigations... - Where west meets east: the complex mtDNA landscape of the southwest and Central Asian corridorLluis Quintana-Murci
Centre National de la Recherche Scientifique CNRS URA 1961, Institut Pasteur, 75724 Paris Cedex 15, France
Am J Hum Genet 74:827-45. 2004.... - Binary and microsatellite polymorphisms of the Y-chromosome in the Mbenzele pygmies from the Central African RepublicValentina Coia
Department of Animal and Human Biology, University La Sapienza, Rome, Italy
Am J Hum Biol 16:57-67. 2004..We suggest that this could be due to the higher phylogenetic stability of Y-chromosome and to the effect of the male-biased gene flow during the Bantu expansion... - Micro-geographical differentiation in Northern Iberia revealed by Y-chromosomal DNA analysisMaria Brion
Institute of Legal Medicine, University of Santiago de Compostela, San Francisco s n, 15782 Santiago de Compostela, Spain
Gene 329:17-25. 2004..Genetic drift in a small isolated population could explain this special behavior, and in addition to its anthropological interest, this finding has important forensic implications... - Phylogeography and origin of Indian domestic goatsManjunath B Joshi
Centre for Cellular and Molecular Biology, Hyderabad, India
Mol Biol Evol 21:454-62. 2004..Thus, we propose a more complex origin for domestic goats... - Y-chromosomal DNA haplogroups and their implications for the dual origins of the KoreansHan-Jun Jin
Department of Biological Sciences, Dankook University, 330-714 Cheonan, Korea
Hum Genet 114:27-35. 2003.... - The human Y chromosome: an evolutionary marker comes of ageMark A Jobling
Department of Genetics, University of Leicester, University Road, Leicester LE1 7RH, UK
Nat Rev Genet 4:598-612. 2003..Y-chromosome research is growing up... - The genetic legacy of the MongolsTatiana Zerjal
Department of Biochemistry, University of Oxford, Oxford, United Kingdom
Am J Hum Genet 72:717-21. 2003..The lineage is carried by likely male-line descendants of Genghis Khan, and we therefore propose that it has spread by a novel form of social selection resulting from their behavior... - A genetic landscape reshaped by recent events: Y-chromosomal insights into central AsiaTatiana Zerjal
Department of Biochemistry, University of Oxford, Oxford, OX1 3QU, United Kingdom
Am J Hum Genet 71:466-82. 2002..Such events could account for the lack of a clear overall pattern and emphasize the importance of multiple recent events in reshaping this genetic landscape... - Y-chromosomal DNA variation in PakistanRaheel Qamar
Biomedical and Genetic Engineering Division, Dr. A. Q. Khan Research Laboratories, Islamabad, Pakistan
Am J Hum Genet 70:1107-24. 2002.... - A predominantly neolithic origin for Y-chromosomal DNA variation in North AfricaBarbara Arredi
Istituto di Medicina Legale, Universita Cattolica del Sacro Cuore di Roma, Rome, Italy
Am J Hum Genet 75:338-45. 2004..Thus, we propose that the Neolithic transition in this part of the world was accompanied by demic diffusion of Afro-Asiatic-speaking pastoralists from the Middle East... - Signature of recent historical events in the European Y-chromosomal STR haplotype distributionLutz Roewer
Institute of Legal Medicine, Humboldt-University, Berlin, Germany
Hum Genet 116:279-91. 2005..We conclude that Y-STRs may be capable of resolving male genealogies to an unparalleled degree and could therefore provide a useful means to study local population structure and recent demographic history... - Y-chromosomal diversity in Lebanon is structured by recent historical eventsPierre A Zalloua
The Lebanese American University, Chouran, Beirut 1102 2801, Lebanon
Am J Hum Genet 82:873-82. 2008.... - Africans in Yorkshire? The deepest-rooting clade of the Y phylogeny within an English genealogyTuri E King
Department of Genetics, University of Leicester, Leicester, UK
Eur J Hum Genet 15:288-93. 2007..Our findings represent the first genetic evidence of Africans among 'indigenous' British, and emphasize the complexity of human migration history as well as the pitfalls of assigning geographical origin from Y-chromosomal haplotypes... - Structural variation on the short arm of the human Y chromosome: recurrent multigene deletions encompassing Amelogenin YMark A Jobling
Department of Genetics, University of Leicester, University Road, Leicester LE1 7RH, UK
Hum Mol Genet 16:307-16. 2007..The persistence and expansion of deletion lineages, together with direct phenotypic evidence, suggests that absence of these genes has no major deleterious effects... - The dawn of human matrilineal diversityDoron M Behar
Molecular Medicine Laboratory, Rambam Health Care Campus, Haifa 31096, Israel
Am J Hum Genet 82:1130-40. 2008..This process was further accelerated during the recent Bantu expansions. Our results suggest that the early settlement of humans in Africa was already matrilineally structured and involved small, separately evolving isolated populations... - Y-chromosomal evidence for a limited Greek contribution to the Pathan population of PakistanSadaf Firasat
Biomedical and Genetic Engineering Division, Dr AQ Khan Research Laboratories, Islamabad, Pakistan
Eur J Hum Genet 15:121-6. 2007..Although based on only a few unrelated descendants, this provides strong evidence for a European origin for a small proportion of the Pathan Y chromosomes... - A shared Y-chromosomal heritage between Muslims and Hindus in IndiaRamana Gutala
Department of Medicine, University of Texas Health Science Center, San Antonio, TX, USA
Hum Genet 120:543-51. 2006..The Muslim expansion in India was predominantly a cultural change and was not accompanied by significant gene flow, as seen in other places, such as China and Central Asia... - Maternal footprints of Southeast Asians in North IndiaKumarasamy Thangaraj
Centre for Cellular and Molecular Biology, Hyderabad, India
Hum Hered 66:1-9. 2008..The presence of R6 in the Nepalese, on the other hand, suggests that the gene flow between India and Nepal has been reciprocal... - Copy number variation: new insights in genome diversityJennifer L Freeman
Department of Pathology, Brigham and Women's Hospital, Boston, Massachusetts 02115, USA
Genome Res 16:949-61. 2006..Current efforts are directed toward a more comprehensive cataloging and characterization of CNVs that will provide the basis for determining how genomic diversity impacts biological function, evolution, and common human diseases... - Hotspots for copy number variation in chimpanzees and humansGeorge H Perry
School of Human Evolution and Social Change, Arizona State University, Tempe, AZ 85287, USA
Proc Natl Acad Sci U S A 103:8006-11. 2006..Therefore, some of these regions may be unstable "hotspots" for the genesis of copy number variation, with recurrent duplications and deletions occurring across and within species... - Male demography in East Asia: a north-south contrast in human population expansion timesYali Xue
Wellcome Trust Sanger Institute, Hinxton, United Kingdom
Genetics 172:2431-9. 2006.... - Hierarchical high-throughput SNP genotyping of the human Y chromosome using MALDI-TOF mass spectrometrySilvia Paracchini
CRC Chromosome Molecular Biology Group, Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, UK
Nucleic Acids Res 30:e27. 2002..The technique thus provides a reliable, cost-effective and automated method for Y genotyping, and the advantages of using a hierarchical strategy can be applied to any DNA segment lacking recombination... - Forensic genetic analysis of mitochondrial DNA hypervariable region I/II sequences: an expanded Korean population databaseHan Jun Jin
Department of Biological Sciences, Dankook University, San 29, Anseo-Dong, Cheonan, Choong-nam 330-714, Republic of Korea
Forensic Sci Int 158:125-30. 2006.... - Y-chromosomal STR haplotypes and their applications to forensic and population studies in east AsiaKyoung Don Kwak
Department of Biological Sciences, Dankook University, Cheonan, 330-714, South Korea
Int J Legal Med 119:195-201. 2005..An admixture estimate suggested 55(51-59)% northern, 45(41-49)% southern contribution to the Koreans, illustrating the complexity of the genetic history of this region... - The Genographic Project public participation mitochondrial DNA databaseDoron M Behar
PLoS Genet 3:e104. 2007..We make available to the scientific community and general public two new resources: a periodically updated database comprising all data donated by participants, and the nearest neighbor haplogroup prediction tool...