Rates of assay success and genotyping error when single nucleotide polymorphism genotyping in non-model organisms: a case study in the Antarctic fur seal
Although single nucleotide polymorphisms (SNPs) are increasingly being recognized as powerful molecular markers, their application to non-model organisms can bring significant challenges. Among these are imperfect conversion rates of assays designed from in silico resources and the enhanced potentia...
Published in: | Molecular Ecology Resources |
---|---|
Main Authors: | , , , , , |
Format: | Article in Journal/Newspaper |
Language: | unknown |
Published: |
Blackwell
2012
|
Subjects: | |
Online Access: | http://nora.nerc.ac.uk/id/eprint/20166/ http://onlinelibrary.wiley.com/doi/10.1111/j.1755-0998.2012.03158.x/abstract |
id |
ftnerc:oai:nora.nerc.ac.uk:20166 |
---|---|
record_format |
openpolar |
spelling |
ftnerc:oai:nora.nerc.ac.uk:20166 2024-02-11T09:58:13+01:00 Rates of assay success and genotyping error when single nucleotide polymorphism genotyping in non-model organisms: a case study in the Antarctic fur seal Hoffman, J.I. Tucker, R. Bridgett, S.J. Clark, M.S. Forcada, J. Slate, J. 2012 http://nora.nerc.ac.uk/id/eprint/20166/ http://onlinelibrary.wiley.com/doi/10.1111/j.1755-0998.2012.03158.x/abstract unknown Blackwell Hoffman, J.I.; Tucker, R.; Bridgett, S.J.; Clark, M.S. orcid:0000-0002-3442-3824 Forcada, J. orcid:0000-0002-2115-0150 Slate, J. 2012 Rates of assay success and genotyping error when single nucleotide polymorphism genotyping in non-model organisms: a case study in the Antarctic fur seal. Molecular Ecology Resources, 12 (5). 861-872. https://doi.org/10.1111/j.1755-0998.2012.03158.x <https://doi.org/10.1111/j.1755-0998.2012.03158.x> Publication - Article PeerReviewed 2012 ftnerc https://doi.org/10.1111/j.1755-0998.2012.03158.x 2024-01-26T00:03:20Z Although single nucleotide polymorphisms (SNPs) are increasingly being recognized as powerful molecular markers, their application to non-model organisms can bring significant challenges. Among these are imperfect conversion rates of assays designed from in silico resources and the enhanced potential for genotyping error relative to pre-validated, highly optimized human SNPs. To explore these issues, we used Illumina’s GoldenGate assay to genotype 480 Antarctic fur seal (Arctocephalus gazella) individuals at 144 putative SNPs derived from a 454 transcriptome assembly. One hundred and thirty-five polymorphic SNPs (93.8%) were automatically validated by the program GenomeStudio, and the initial genotyping error rate, estimated from nine replicate samples, was 0.004 per reaction. However, an almost tenfold further reduction in the error rate was achieved by excluding 31 loci (21.5%) that exhibited unclear clustering patterns, manually editing clusters to allow rescoring of ambiguous or incorrect genotypes, and excluding 18 samples (3.8%) with unreliable genotypes. After stringent quality filtering, we also found a counter-intuitive negative relationship between in silico minor allele frequency and the conversion rate, suggesting that some of our assays may have been designed from paralogous loci. Nevertheless, we obtained over 45 000 individual SNP genotypes with a final error rate of 0.0005, indicating that the GoldenGate assay is eminently capable of generating large, high-quality data sets for non-model organisms. This has positive implications for future studies of the evolutionary, behavioural and conservation genetics of natural populations. Article in Journal/Newspaper Antarc* Antarctic Antarctic Fur Seal Arctocephalus gazella Natural Environment Research Council: NERC Open Research Archive Antarctic The Antarctic Molecular Ecology Resources 12 5 861 872 |
institution |
Open Polar |
collection |
Natural Environment Research Council: NERC Open Research Archive |
op_collection_id |
ftnerc |
language |
unknown |
description |
Although single nucleotide polymorphisms (SNPs) are increasingly being recognized as powerful molecular markers, their application to non-model organisms can bring significant challenges. Among these are imperfect conversion rates of assays designed from in silico resources and the enhanced potential for genotyping error relative to pre-validated, highly optimized human SNPs. To explore these issues, we used Illumina’s GoldenGate assay to genotype 480 Antarctic fur seal (Arctocephalus gazella) individuals at 144 putative SNPs derived from a 454 transcriptome assembly. One hundred and thirty-five polymorphic SNPs (93.8%) were automatically validated by the program GenomeStudio, and the initial genotyping error rate, estimated from nine replicate samples, was 0.004 per reaction. However, an almost tenfold further reduction in the error rate was achieved by excluding 31 loci (21.5%) that exhibited unclear clustering patterns, manually editing clusters to allow rescoring of ambiguous or incorrect genotypes, and excluding 18 samples (3.8%) with unreliable genotypes. After stringent quality filtering, we also found a counter-intuitive negative relationship between in silico minor allele frequency and the conversion rate, suggesting that some of our assays may have been designed from paralogous loci. Nevertheless, we obtained over 45 000 individual SNP genotypes with a final error rate of 0.0005, indicating that the GoldenGate assay is eminently capable of generating large, high-quality data sets for non-model organisms. This has positive implications for future studies of the evolutionary, behavioural and conservation genetics of natural populations. |
format |
Article in Journal/Newspaper |
author |
Hoffman, J.I. Tucker, R. Bridgett, S.J. Clark, M.S. Forcada, J. Slate, J. |
spellingShingle |
Hoffman, J.I. Tucker, R. Bridgett, S.J. Clark, M.S. Forcada, J. Slate, J. Rates of assay success and genotyping error when single nucleotide polymorphism genotyping in non-model organisms: a case study in the Antarctic fur seal |
author_facet |
Hoffman, J.I. Tucker, R. Bridgett, S.J. Clark, M.S. Forcada, J. Slate, J. |
author_sort |
Hoffman, J.I. |
title |
Rates of assay success and genotyping error when single nucleotide polymorphism genotyping in non-model organisms: a case study in the Antarctic fur seal |
title_short |
Rates of assay success and genotyping error when single nucleotide polymorphism genotyping in non-model organisms: a case study in the Antarctic fur seal |
title_full |
Rates of assay success and genotyping error when single nucleotide polymorphism genotyping in non-model organisms: a case study in the Antarctic fur seal |
title_fullStr |
Rates of assay success and genotyping error when single nucleotide polymorphism genotyping in non-model organisms: a case study in the Antarctic fur seal |
title_full_unstemmed |
Rates of assay success and genotyping error when single nucleotide polymorphism genotyping in non-model organisms: a case study in the Antarctic fur seal |
title_sort |
rates of assay success and genotyping error when single nucleotide polymorphism genotyping in non-model organisms: a case study in the antarctic fur seal |
publisher |
Blackwell |
publishDate |
2012 |
url |
http://nora.nerc.ac.uk/id/eprint/20166/ http://onlinelibrary.wiley.com/doi/10.1111/j.1755-0998.2012.03158.x/abstract |
geographic |
Antarctic The Antarctic |
geographic_facet |
Antarctic The Antarctic |
genre |
Antarc* Antarctic Antarctic Fur Seal Arctocephalus gazella |
genre_facet |
Antarc* Antarctic Antarctic Fur Seal Arctocephalus gazella |
op_relation |
Hoffman, J.I.; Tucker, R.; Bridgett, S.J.; Clark, M.S. orcid:0000-0002-3442-3824 Forcada, J. orcid:0000-0002-2115-0150 Slate, J. 2012 Rates of assay success and genotyping error when single nucleotide polymorphism genotyping in non-model organisms: a case study in the Antarctic fur seal. Molecular Ecology Resources, 12 (5). 861-872. https://doi.org/10.1111/j.1755-0998.2012.03158.x <https://doi.org/10.1111/j.1755-0998.2012.03158.x> |
op_doi |
https://doi.org/10.1111/j.1755-0998.2012.03158.x |
container_title |
Molecular Ecology Resources |
container_volume |
12 |
container_issue |
5 |
container_start_page |
861 |
op_container_end_page |
872 |
_version_ |
1790593817670320128 |