Imperial College London

DrLachlanCoin

Faculty of MedicineDepartment of Medicine

Honorary Senior Lecturer
 
 
 
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Contact

 

+44 (0)20 7594 1930l.coin

 
 
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Location

 

172Medical SchoolSt Mary's Campus

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Summary

 

Summary

I am  working on various statistical and mathematical problems in genomics. I am particularly interested in building mathematical models to identify genetic variants in high-throughput genomics data - including genotyping microarrays and next generation sequence data - with the ultimate aim of understanding the functional impact and evolutionary history of these variants.

Software can be found on my github page:
https://github.com/lachlancoin

More information:
https://orcid.org/0000-0002-4300-455X

ECCB 2012 report

Software:  

Yhap  software for identifying haplogroups from low coverage sequence data: Yhap_0.51

ExomeCNVTest software : ExomeCNVTest_0.51

SOAP-popIndel  software for genotyping indels in exome data

SOAP-popIndel

cnvHiTSeq - software for detecting and genotyping CNVs in WGS data: cnvHitSeq

Toy example for cnvHitSeq

cnvPipe - software to enable CNV meta analysis: cnvPipe_v0.82

Software for converting  IMPUTE format to format used by MultiPhen software: convertImpute

MultiPhen software: MultiPhen

vntrTest:
vntrTest is a program for assessing association of VNTR fragment length genotypes with either continuous or case-control outcomes. 

VNTRTest0.52

cnvHap:
cnvHap is a program for joint copy number genotyping, which uses a haplotype model of copy number variation and integrates data from multiple platforms. It also carries out CN association.

cnvHapv1.033

polyHap
polyHap is a program for phasing polyploids and copy number regions.

See http://dx.doi.org/10.1186/1471-2105-9-513 for more details.

The first version was designed just for phasing polyploid regions (with the restriction that the ploidy is fixed across the entire region of analysis).

polyHap(v1)

We have extended polyHap to remove this restriction, so that it can phase CNV regions (from pre-calculated CNV/SNP genotypes):

polyHap(v2)

AncesHC
AncesHC is a program for determining the haplotype structure of a population sample from genotype data, and then testing for association of these haplotypes with either a binary or continous outcome.

See http://dx.doi.org/10.1093/bioinformatics/btn071 for more details.

AncesHC2009_1

metaMapper
metaMapper is a program for flexible, scalable GWAS meta-analysis and visualisation.

MetaMapper_1.01

invertFREGENE
Software for simulating sequence level data with inversions. See http://dx.doi.org/10.1093/bioinformatics/btq029 for more details. Developed in conjunction with Clive Hoggart and Paul O'Reilly.

invertFREGENE.pdf

invertFREGENE.tar.gz

Pseudogene inference from loss of constraint (PSILC)
Software for identifying pseudogenes via loss of evolutionary constraint:

PSILC version 1.21

Supplementary data
Supplementary information from paper "Pathway Analysis of GWAS Provides New Insights into Genetic Susceptibility to 3 Inflammatory Diseases"

Publications

Journals

Poznik GD, Xue Y, Mendez FL, et al., 2016, Punctuated bursts in human male demography inferred from 1,244 worldwide Y-chromosome sequences, Nature Genetics, Vol:48, ISSN:1061-4036, Pages:593-+

Elliott AG, Ganesamoorthy D, Coin L, et al., 2016, Complete Genome Sequence of Klebsiella quasipneumoniae subsp. similipneumoniae Strain ATCC 700603., Genome Announc, Vol:4, ISSN:2169-8287

Li J, Woods SL, Healey S, et al., 2016, Point Mutations in Exon 1B of APC Reveal Gastric Adenocarcinoma and Proximal Polyposis of the Stomach as a Familial Adenomatous Polyposis Variant, American Journal of Human Genetics, Vol:98, ISSN:0002-9297, Pages:830-842

Minh DC, Ganesamoorthy D, Cooper MA, et al., 2016, Realtime analysis and visualization of MinION sequencing data with npReader, Bioinformatics, Vol:32, ISSN:1367-4803, Pages:764-766

Altshuler DM, Durbin RM, Abecasis GR, et al., 2015, A global reference for human genetic variation, Nature, Vol:526, ISSN:0028-0836, Pages:68-+

More Publications