Search

Your search keyword '"SNP informativeness"' showing total 4 results
Start Over Descriptor "SNP informativeness"
4 results on '"SNP informativeness"'

1. Developing a 670k genotyping array to tag ~2M SNPs across 24 horse breeds

Author

Schaefer, Robert J, Schubert, Mikkel, Bailey, Ernest, Bannasch, Danika L, Barrey, Eric, Bar-Gal, Gila Kahila, Brem, Gottfried, Brooks, Samantha A, Distl, Ottmar, Fries, Ruedi, Finno, Carrie J, Gerber, Vinzenz, Haase, Bianca, Jagannathan, Vidhya, Kalbfleisch, Ted, Leeb, Tosso, Lindgren, Gabriella, Lopes, Maria Susana, Mach, Núria, da Câmara Machado, Artur, MacLeod, James N, McCoy, Annette, Metzger, Julia, Penedo, Cecilia, Polani, Sagi, Rieder, Stefan, Tammen, Imke, Tetens, Jens, Thaller, Georg, Verini-Supplizi, Andrea, Wade, Claire M, Wallner, Barbara, Orlando, Ludovic, Mickelson, James R, and McCue, Molly E

Subjects
Biological Sciences, Bioinformatics and Computational Biology, Genetics, Human Genome, Biotechnology, Animals, Gene Frequency, Genotyping Techniques, Horses, Linkage Disequilibrium, Oligonucleotide Array Sequence Analysis, Polymorphism, Single Nucleotide, Reference Standards, Whole Genome Sequencing, Equine genomics, Whole genome sequence, SNP-tagging, SNP chip, Variant recalibration, SNP discovery, SNP informativeness, SNP validation, Linkage disequilibrium, Information and Computing Sciences, Medical and Health Sciences, Bioinformatics, Biological sciences, Biomedical and clinical sciences
Abstract

BackgroundTo date, genome-scale analyses in the domestic horse have been limited by suboptimal single nucleotide polymorphism (SNP) density and uneven genomic coverage of the current SNP genotyping arrays. The recent availability of whole genome sequences has created the opportunity to develop a next generation, high-density equine SNP array.ResultsUsing whole genome sequence from 153 individuals representing 24 distinct breeds collated by the equine genomics community, we cataloged over 23 million de novo discovered genetic variants. Leveraging genotype data from individuals with both whole genome sequence, and genotypes from lower-density, legacy SNP arrays, a subset of ~5 million high-quality, high-density array candidate SNPs were selected based on breed representation and uniform spacing across the genome. Considering probe design recommendations from a commercial vendor (Affymetrix, now Thermo Fisher Scientific) a set of ~2 million SNPs were selected for a next-generation high-density SNP chip (MNEc2M). Genotype data were generated using the MNEc2M array from a cohort of 332 horses from 20 breeds and a lower-density array, consisting of ~670 thousand SNPs (MNEc670k), was designed for genotype imputation.ConclusionsHere, we document the steps taken to design both the MNEc2M and MNEc670k arrays, report genomic and technical properties of these genotyping platforms, and demonstrate the imputation capabilities of these tools for the domestic horse.

Published
2017

2. Developing a 670k genotyping array to tag ~2M SNPs across 24 horse breeds

Author

Schaefer, Robert J., Schubert, Mikkel, Bailey, Ernest, Bannasch, Danika L., Barrey, Eric, Bar-Gal, Gila Kahila, Brem, Gottfried, Brooks, Samantha A., Distl, Ottmar, Fries, Ruedi, Finno, Carrie J., Gerber, Vinzenz, Haase, Bianca, Jagannathan, Vidhya, Kalbfleisch, Ted, Leeb, Tosso, Lindgren, Gabriella, Lopes, Maria Susana, Mach, Núria, Machado, Artur da Câmara, MacLeod, James N., McCoy, Annette, Metzger, Julia, Penedo, Cecilia, Polani, Sagi, Rieder, Stefan, Tammen, Imke, Tetens, Jens, Thaller, Georg, Verini-Supplizi, Andrea, Wade, Claire, Wallner, Barbara, Orlando, Ludovic Antoine Alexandre, Mickelson, James R., McCue, Molly E., Schaefer, Robert J., Schubert, Mikkel, Bailey, Ernest, Bannasch, Danika L., Barrey, Eric, Bar-Gal, Gila Kahila, Brem, Gottfried, Brooks, Samantha A., Distl, Ottmar, Fries, Ruedi, Finno, Carrie J., Gerber, Vinzenz, Haase, Bianca, Jagannathan, Vidhya, Kalbfleisch, Ted, Leeb, Tosso, Lindgren, Gabriella, Lopes, Maria Susana, Mach, Núria, Machado, Artur da Câmara, MacLeod, James N., McCoy, Annette, Metzger, Julia, Penedo, Cecilia, Polani, Sagi, Rieder, Stefan, Tammen, Imke, Tetens, Jens, Thaller, Georg, Verini-Supplizi, Andrea, Wade, Claire, Wallner, Barbara, Orlando, Ludovic Antoine Alexandre, Mickelson, James R., and McCue, Molly E.

Published
2017

3. Developing a 670k genotyping array to tag ~2M SNPs across 24 horse breeds

Author

M. S. Lopes, Barbara Wallner, Ted Kalbfleisch, Julia Metzger, Claire M. Wade, Cecilia Penedo, James N. MacLeod, Sagi Polani, Molly E. McCue, Gila Kahila Bar-Gal, Tosso Leeb, James R. Mickelson, Gottfried Brem, Ludovic Orlando, Mikkel Schubert, Annette M. McCoy, Bianca Haase, Núria Mach, Eric Barrey, Vidhya Jagannathan, Jens Tetens, Carrie J. Finno, Ottmar Distl, Georg Thaller, Samantha A. Brooks, Andrea Verini-Supplizi, Artur da Câmara Machado, Danika L. Bannasch, Ruedi Fries, Robert J. Schaefer, Imke Tammen, Ernest Bailey, Stefan Rieder, Vinzenz Gerber, and Gabriella Lindgren

Subjects
0301 basic medicine, Genotyping Techniques, SNP validation, Genome, Medical and Health Sciences, Linkage Disequilibrium, Gene Frequency, Equine genomics, Linkage disequilibrium, SNP chip, SNP discovery, SNP informativeness, SNP-tagging, Variant recalibration, Whole genome sequence, Biotechnology, Genetics, Oligonucleotide Array Sequence Analysis, 2. Zero hunger, 0303 health sciences, 630 Agriculture, 04 agricultural and veterinary sciences, Single Nucleotide, Tag SNP, Reference Standards, Biological Sciences, SNP genotyping, 590 Animals (Zoology), Research Article, SNP array, lcsh:QH426-470, Bioinformatics, lcsh:Biotechnology, Single-nucleotide polymorphism, Genomics, 610 Medicine & health, Computational biology, Biology, Polymorphism, Single Nucleotide, 03 medical and health sciences, lcsh:TP248.13-248.65, Information and Computing Sciences, Animals, Horses, Polymorphism, Genotyping, 030304 developmental biology, Whole genome sequencing, Whole Genome Sequencing, Human Genome, 0402 animal and dairy science, 040201 dairy & animal science, lcsh:Genetics, 030104 developmental biology, 570 Life sciences, biology, Imputation (genetics)
Abstract

BackgroundTo date, genome-scale analyses in the domestic horse have been limited by suboptimal single nucleotide polymorphism (SNP) density and uneven genomic coverage of the current SNP genotyping arrays. The recent availability of whole genome sequences has created the opportunity to develop a next generation, high-density equine SNP array.ResultsUsing whole genome sequence from 153 individuals representing 24 distinct breeds collated by the equine genomics community, we cataloged over 23 millionde novodiscovered genetic variants. Leveraging genotype data from individuals with both whole genome sequence, and genotypes from lower-density, legacy SNP arrays, a subset of ∼5 million high-quality, high-density array candidate SNPs were selected based on breed representation and uniform spacing across the genome. Considering probe design recommendations from a commercial vendor (Affymetrix, now Thermo Fisher Scientific) a set of ∼2 million SNPs were selected for a next-generation high-density SNP chip (MNEc2M). Genotype data were generated using the MNEc2M array from a cohort of 332 horses from 20 breeds and a lower-density array, consisting of ∼670 thousand SNPs (MNEc670k), was designed for genotype imputation.ConclusionsHere, we document the steps taken to design both the MNEc2M and MNEc670k arrays, report genomic and technical properties of these genotyping platforms, and demonstrate the imputation capabilities of these tools for the domestic horse.

Published
2017

4. Developing a 670k genotyping array to tag similar to 2M SNPs across 24 horse breeds

Author

Schaefer, Robert J, Schubert, Mikkel K, Bailey, Ernest K, Bannasch, Danika L, Barrey, Eric, Bar-Gal, Gila Kahila, Brem, Gottfried J, Brooks, Samantha A, Distl, Ottmar K, Fries, Ruedi K, Finno, Carrie J, Gerber, Vinzenz K, Haase, Bianca K, Jagannathan, Vidhya K, Kalbfleisch, Ted K, Leeb, Tosso K, Lindgren, Gabriella K, Lopes, Maria Susana, Mach Casellas, Nuria, Machado, Artur daCamara, MacLeod, James N, McCoy, Annette K, Metzger, Julia K, Penedo, Cecilia K, Polani, Sagi K, Rieder, Stefan K, Tammen, Imke K, Tetens, Jens K, Thaller, Georg P, Verini-Supplizi, Andrea P, Wade, Claire M, Wallner, Barbara T, Orlando, Ludovic, Mickelson, James R, and McCue, Molly E

Subjects
Equine genomics, Whole genome sequence, SNP-tagging, SNP chip, Variant recalibration, SNP discovery, SNP informativeness, SNP validation, Linkage disequilibrium
Abstract

Background: To date, genome-scale analyses in the domestic horse have been limited by suboptimal single nucleotide polymorphism (SNP) density and uneven genomic coverage of the current SNP genotyping arrays. The recent availability of whole genome sequences has created the opportunity to develop a next generation, high-density equine SNP array. Results: Using whole genome sequence from 153 individuals representing 24 distinct breeds collated by the equine genomics community, we cataloged over 23 million de novo discovered genetic variants. Leveraging genotype data from individuals with both whole genome sequence, and genotypes from lower-density, legacy SNP arrays, a subset of similar to 5 million high-quality, high-density array candidate SNPs were selected based on breed representation and uniform spacing across the genome. Considering probe design recommendations from a commercial vendor (Affymetrix, now Thermo Fisher Scientific) a set of similar to 2 million SNPs were selected for a next-generation high-density SNP chip (MNEc2M). Genotype data were generated using the MNEc2M array from a cohort of 332 horses from 20 breeds and a lower-density array, consisting of similar to 670 thousand SNPs (MNEc670k), was designed for genotype imputation. Conclusions: Here, we document the steps taken to design both the MNEc2M and MNEc670k arrays, report genomic and technical properties of these genotyping platforms, and demonstrate the imputation capabilities of these tools for the domestic horse.

Published
2017

Catalog

Books, media, physical & digital resources
See catalog results