Transcriptomic SNP discovery for custom genotyping arrays: impacts of sequence data, SNP calling method and genotyping technology on the probability of validation success
Background Single nucleotide polymorphism (SNP) discovery is an important goal of many studies. However, the number of ‘putative’ SNPs discovered from a sequence resource may not provide a reliable indication of the number that will successfully validate with a given genotyping technology. For this...
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ftnerc:oai:nora.nerc.ac.uk:514399 2023-05-15T13:49:33+02:00 Transcriptomic SNP discovery for custom genotyping arrays: impacts of sequence data, SNP calling method and genotyping technology on the probability of validation success Humble, Emily Thorne, Michael A.S. Forcada, Jaume Hoffman, Joseph I. 2016-08 text http://nora.nerc.ac.uk/id/eprint/514399/ https://nora.nerc.ac.uk/id/eprint/514399/1/Humble.pdf https://doi.org/10.1186/s13104-016-2209-x en eng BioMed Central https://nora.nerc.ac.uk/id/eprint/514399/1/Humble.pdf Humble, Emily; Thorne, Michael A.S. orcid:0000-0001-7759-612X Forcada, Jaume orcid:0000-0002-2115-0150 Hoffman, Joseph I. 2016 Transcriptomic SNP discovery for custom genotyping arrays: impacts of sequence data, SNP calling method and genotyping technology on the probability of validation success. BMC Research Notes, 9 (1), 418. 12, pp. https://doi.org/10.1186/s13104-016-2209-x <https://doi.org/10.1186/s13104-016-2209-x> cc_by_4 CC-BY Publication - Article PeerReviewed 2016 ftnerc https://doi.org/10.1186/s13104-016-2209-x 2023-02-04T19:43:29Z Background Single nucleotide polymorphism (SNP) discovery is an important goal of many studies. However, the number of ‘putative’ SNPs discovered from a sequence resource may not provide a reliable indication of the number that will successfully validate with a given genotyping technology. For this it may be necessary to account for factors such as the method used for SNP discovery and the type of sequence data from which it originates, suitability of the SNP flanking sequences for probe design, and genomic context. To explore the relative importance of these and other factors, we used Illumina sequencing to augment an existing Roche 454 transcriptome assembly for the Antarctic fur seal (Arctocephalus gazella). We then mapped the raw Illumina reads to the new hybrid transcriptome using BWA and BOWTIE2 before calling SNPs with GATK. The resulting markers were pooled with two existing sets of SNPs called from the original 454 assembly using NEWBLER and SWAP454. Finally, we explored the extent to which SNPs discovered using these four methods overlapped and predicted the corresponding validation outcomes for both Illumina Infinium iSelect HD and Affymetrix Axiom arrays. Results Collating markers across all discovery methods resulted in a global list of 34,718 SNPs. However, concordance between the methods was surprisingly poor, with only 51.0 % of SNPs being discovered by more than one method and 13.5 % being called from both the 454 and Illumina datasets. Using a predictive modeling approach, we could also show that SNPs called from the Illumina data were on average more likely to successfully validate, as were SNPs called by more than one method. Above and beyond this pattern, predicted validation outcomes were also consistently better for Affymetrix Axiom arrays. Conclusions Our results suggest that focusing on SNPs called by more than one method could potentially improve validation outcomes. They also highlight possible differences between alternative genotyping technologies that could be explored in future ... Article in Journal/Newspaper Antarc* Antarctic Antarctic Fur Seal Arctocephalus gazella Natural Environment Research Council: NERC Open Research Archive Antarctic The Antarctic BMC Research Notes 9 1 |
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Open Polar |
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Natural Environment Research Council: NERC Open Research Archive |
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ftnerc |
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English |
description |
Background Single nucleotide polymorphism (SNP) discovery is an important goal of many studies. However, the number of ‘putative’ SNPs discovered from a sequence resource may not provide a reliable indication of the number that will successfully validate with a given genotyping technology. For this it may be necessary to account for factors such as the method used for SNP discovery and the type of sequence data from which it originates, suitability of the SNP flanking sequences for probe design, and genomic context. To explore the relative importance of these and other factors, we used Illumina sequencing to augment an existing Roche 454 transcriptome assembly for the Antarctic fur seal (Arctocephalus gazella). We then mapped the raw Illumina reads to the new hybrid transcriptome using BWA and BOWTIE2 before calling SNPs with GATK. The resulting markers were pooled with two existing sets of SNPs called from the original 454 assembly using NEWBLER and SWAP454. Finally, we explored the extent to which SNPs discovered using these four methods overlapped and predicted the corresponding validation outcomes for both Illumina Infinium iSelect HD and Affymetrix Axiom arrays. Results Collating markers across all discovery methods resulted in a global list of 34,718 SNPs. However, concordance between the methods was surprisingly poor, with only 51.0 % of SNPs being discovered by more than one method and 13.5 % being called from both the 454 and Illumina datasets. Using a predictive modeling approach, we could also show that SNPs called from the Illumina data were on average more likely to successfully validate, as were SNPs called by more than one method. Above and beyond this pattern, predicted validation outcomes were also consistently better for Affymetrix Axiom arrays. Conclusions Our results suggest that focusing on SNPs called by more than one method could potentially improve validation outcomes. They also highlight possible differences between alternative genotyping technologies that could be explored in future ... |
format |
Article in Journal/Newspaper |
author |
Humble, Emily Thorne, Michael A.S. Forcada, Jaume Hoffman, Joseph I. |
spellingShingle |
Humble, Emily Thorne, Michael A.S. Forcada, Jaume Hoffman, Joseph I. Transcriptomic SNP discovery for custom genotyping arrays: impacts of sequence data, SNP calling method and genotyping technology on the probability of validation success |
author_facet |
Humble, Emily Thorne, Michael A.S. Forcada, Jaume Hoffman, Joseph I. |
author_sort |
Humble, Emily |
title |
Transcriptomic SNP discovery for custom genotyping arrays: impacts of sequence data, SNP calling method and genotyping technology on the probability of validation success |
title_short |
Transcriptomic SNP discovery for custom genotyping arrays: impacts of sequence data, SNP calling method and genotyping technology on the probability of validation success |
title_full |
Transcriptomic SNP discovery for custom genotyping arrays: impacts of sequence data, SNP calling method and genotyping technology on the probability of validation success |
title_fullStr |
Transcriptomic SNP discovery for custom genotyping arrays: impacts of sequence data, SNP calling method and genotyping technology on the probability of validation success |
title_full_unstemmed |
Transcriptomic SNP discovery for custom genotyping arrays: impacts of sequence data, SNP calling method and genotyping technology on the probability of validation success |
title_sort |
transcriptomic snp discovery for custom genotyping arrays: impacts of sequence data, snp calling method and genotyping technology on the probability of validation success |
publisher |
BioMed Central |
publishDate |
2016 |
url |
http://nora.nerc.ac.uk/id/eprint/514399/ https://nora.nerc.ac.uk/id/eprint/514399/1/Humble.pdf https://doi.org/10.1186/s13104-016-2209-x |
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 |
https://nora.nerc.ac.uk/id/eprint/514399/1/Humble.pdf Humble, Emily; Thorne, Michael A.S. orcid:0000-0001-7759-612X Forcada, Jaume orcid:0000-0002-2115-0150 Hoffman, Joseph I. 2016 Transcriptomic SNP discovery for custom genotyping arrays: impacts of sequence data, SNP calling method and genotyping technology on the probability of validation success. BMC Research Notes, 9 (1), 418. 12, pp. https://doi.org/10.1186/s13104-016-2209-x <https://doi.org/10.1186/s13104-016-2209-x> |
op_rights |
cc_by_4 |
op_rightsnorm |
CC-BY |
op_doi |
https://doi.org/10.1186/s13104-016-2209-x |
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BMC Research Notes |
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9 |
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1 |
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1766251543479189504 |