Integration of Infinium and Axiom SNP array data in the outcrossing species Malus × domestica and causes for seemingly incompatible calls
Abstract Background Single nucleotide polymorphism (SNP) array technology has been increasingly used to generate large quantities of SNP data for use in genetic studies. As new arrays are developed to take advantage of new technology and of improved probe design using new genome sequence and panel d...
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| Format: | Article |
| Language: | English |
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BMC
2021-04-01
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| Series: | BMC Genomics |
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| Online Access: | https://doi.org/10.1186/s12864-021-07565-7 |
| _version_ | 1818329453557710848 |
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| author | Nicholas P. Howard Michela Troggio Charles-Eric Durel Hélène Muranty Caroline Denancé Luca Bianco John Tillman Eric van de Weg |
| author_facet | Nicholas P. Howard Michela Troggio Charles-Eric Durel Hélène Muranty Caroline Denancé Luca Bianco John Tillman Eric van de Weg |
| author_sort | Nicholas P. Howard |
| collection | DOAJ |
| description | Abstract Background Single nucleotide polymorphism (SNP) array technology has been increasingly used to generate large quantities of SNP data for use in genetic studies. As new arrays are developed to take advantage of new technology and of improved probe design using new genome sequence and panel data, a need to integrate data from different arrays and array platforms has arisen. This study was undertaken in view of our need for an integrated high-quality dataset of Illumina Infinium® 20 K and Affymetrix Axiom® 480 K SNP array data in apple (Malus × domestica). In this study, we qualify and quantify the compatibility of SNP calling, defined as SNP calls that are both accurate and concordant, across both arrays by two approaches. First, the concordance of SNP calls was evaluated using a set of 417 duplicate individuals genotyped on both arrays starting from a set of 10,295 robust SNPs on the Infinium array. Next, the accuracy of the SNP calls was evaluated on additional germplasm (n = 3141) from both arrays using Mendelian inconsistent and consistent errors across thousands of pedigree links. While performing this work, we took the opportunity to evaluate reasons for probe failure and observed discordant SNP calls. Results Concordance among the duplicate individuals was on average of 97.1% across 10,295 SNPs. Of these SNPs, 35% had discordant call(s) that were further curated, leading to a final set of 8412 (81.7%) SNPs that were deemed compatible. Compatibility was highly influenced by the presence of alternate probe binding locations and secondary polymorphisms. The impact of the latter was highly influenced by their number and proximity to the 3′ end of the probe. Conclusions The Infinium and Axiom SNP array data were mostly compatible. However, data integration required intense data filtering and curation. This work resulted in a workflow and information that may be of use in other data integration efforts. Such an in-depth analysis of array concordance and accuracy as ours has not been previously described in the literature and will be useful in future work on SNP array data integration and interpretation, and in probe/platform development. |
| first_indexed | 2024-12-13T12:48:18Z |
| format | Article |
| id | doaj.art-81942d51737347cdb87573851e253f5b |
| institution | Directory Open Access Journal |
| issn | 1471-2164 |
| language | English |
| last_indexed | 2024-12-13T12:48:18Z |
| publishDate | 2021-04-01 |
| publisher | BMC |
| record_format | Article |
| series | BMC Genomics |
| spelling | doaj.art-81942d51737347cdb87573851e253f5b2022-12-21T23:45:25ZengBMCBMC Genomics1471-21642021-04-0122111810.1186/s12864-021-07565-7Integration of Infinium and Axiom SNP array data in the outcrossing species Malus × domestica and causes for seemingly incompatible callsNicholas P. Howard0Michela Troggio1Charles-Eric Durel2Hélène Muranty3Caroline Denancé4Luca Bianco5John Tillman6Eric van de Weg7Institut für Biologie und Umweltwissenschaften, Carl von Ossietzky Univ.Fondazione Edmund MachUniversité d’Angers, Institut Agro, INRAE, IRHS, SFR 4207 QuaSaVUniversité d’Angers, Institut Agro, INRAE, IRHS, SFR 4207 QuaSaVUniversité d’Angers, Institut Agro, INRAE, IRHS, SFR 4207 QuaSaVFondazione Edmund MachDepartment of Horticultural Science, Univ. of MinnesotaDepartment of Plant Breeding, Wageningen University and ResearchAbstract Background Single nucleotide polymorphism (SNP) array technology has been increasingly used to generate large quantities of SNP data for use in genetic studies. As new arrays are developed to take advantage of new technology and of improved probe design using new genome sequence and panel data, a need to integrate data from different arrays and array platforms has arisen. This study was undertaken in view of our need for an integrated high-quality dataset of Illumina Infinium® 20 K and Affymetrix Axiom® 480 K SNP array data in apple (Malus × domestica). In this study, we qualify and quantify the compatibility of SNP calling, defined as SNP calls that are both accurate and concordant, across both arrays by two approaches. First, the concordance of SNP calls was evaluated using a set of 417 duplicate individuals genotyped on both arrays starting from a set of 10,295 robust SNPs on the Infinium array. Next, the accuracy of the SNP calls was evaluated on additional germplasm (n = 3141) from both arrays using Mendelian inconsistent and consistent errors across thousands of pedigree links. While performing this work, we took the opportunity to evaluate reasons for probe failure and observed discordant SNP calls. Results Concordance among the duplicate individuals was on average of 97.1% across 10,295 SNPs. Of these SNPs, 35% had discordant call(s) that were further curated, leading to a final set of 8412 (81.7%) SNPs that were deemed compatible. Compatibility was highly influenced by the presence of alternate probe binding locations and secondary polymorphisms. The impact of the latter was highly influenced by their number and proximity to the 3′ end of the probe. Conclusions The Infinium and Axiom SNP array data were mostly compatible. However, data integration required intense data filtering and curation. This work resulted in a workflow and information that may be of use in other data integration efforts. Such an in-depth analysis of array concordance and accuracy as ours has not been previously described in the literature and will be useful in future work on SNP array data integration and interpretation, and in probe/platform development.https://doi.org/10.1186/s12864-021-07565-7SNP ArraySingle nucleotide polymorphismGenotypingMalus |
| spellingShingle | Nicholas P. Howard Michela Troggio Charles-Eric Durel Hélène Muranty Caroline Denancé Luca Bianco John Tillman Eric van de Weg Integration of Infinium and Axiom SNP array data in the outcrossing species Malus × domestica and causes for seemingly incompatible calls BMC Genomics SNP Array Single nucleotide polymorphism Genotyping Malus |
| title | Integration of Infinium and Axiom SNP array data in the outcrossing species Malus × domestica and causes for seemingly incompatible calls |
| title_full | Integration of Infinium and Axiom SNP array data in the outcrossing species Malus × domestica and causes for seemingly incompatible calls |
| title_fullStr | Integration of Infinium and Axiom SNP array data in the outcrossing species Malus × domestica and causes for seemingly incompatible calls |
| title_full_unstemmed | Integration of Infinium and Axiom SNP array data in the outcrossing species Malus × domestica and causes for seemingly incompatible calls |
| title_short | Integration of Infinium and Axiom SNP array data in the outcrossing species Malus × domestica and causes for seemingly incompatible calls |
| title_sort | integration of infinium and axiom snp array data in the outcrossing species malus domestica and causes for seemingly incompatible calls |
| topic | SNP Array Single nucleotide polymorphism Genotyping Malus |
| url | https://doi.org/10.1186/s12864-021-07565-7 |
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