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1. Characterization of a Homozygous Deletion of Steroid Hormone Biosynthesis Genes in Horse Chromosome 29 as a Risk Factor for Disorders of Sex Development and Reproduction

Author

Ghosh, Sharmila, Davis, Brian W, Rosengren, Maria, Jevit, Matthew J, Castaneda, Caitlin, Arnold, Carolyn, Jaxheimer, Jay, Love, Charles C, Varner, Dickson D, Lindgren, Gabriella, Wade, Claire M, and Raudsepp, Terje

Subjects
Human Genome, Genetics, Aetiology, 2.1 Biological and endogenous factors, Reproductive health and childbirth, Animals, Breeding, Chromosomes, Disorders of Sex Development, Genotype, Gonadal Steroid Hormones, Homozygote, Horses, Polymorphism, Single Nucleotide, Reproduction, Risk Factors, Sequence Deletion, Sexual Development, horse, disorders of sex development, cryptorchidism, reproduction, CNV, ECA29, steroid hormone, AKR1C
Abstract

Disorders of sex development (DSD) and reproduction are not uncommon among horses, though knowledge about their molecular causes is sparse. Here we characterized a ~200 kb homozygous deletion in chromosome 29 at 29.7-29.9 Mb. The region contains AKR1C genes which function as ketosteroid reductases in steroid hormone biosynthesis, including androgens and estrogens. Mutations in AKR1C genes are associated with human DSDs. Deletion boundaries, sequence properties and gene content were studied by PCR and whole genome sequencing of select deletion homozygotes and control animals. Deletion analysis by PCR in 940 horses, including 622 with DSDs and reproductive problems and 318 phenotypically normal controls, detected 67 deletion homozygotes of which 79% were developmentally or reproductively abnormal. Altogether, 8-9% of all abnormal horses were homozygous for the deletion, with the highest incidence (9.4%) among cryptorchids. The deletion was found in ~4% of our phenotypically normal cohort, ~1% of global warmblood horses and ponies, and ~7% of draught breeds of general horse population as retrieved from published data. Based on the abnormal phenotype of the carriers, the functionally relevant gene content, and the low incidence in general population, we consider the deletion in chromosome 29 as a risk factor for equine DSDs and reproductive disorders.

Published
2020

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, 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

3. Genome-wide association studies in dogs and humans identify ADAMTS20 as a risk variant for cleft lip and palate.

Author

Wolf, Zena T, Brand, Harrison A, Shaffer, John R, Leslie, Elizabeth J, Arzi, Boaz, Willet, Cali E, Cox, Timothy C, McHenry, Toby, Narayan, Nicole, Feingold, Eleanor, Wang, Xioajing, Sliskovic, Saundra, Karmi, Nili, Safra, Noa, Sanchez, Carla, Deleyiannis, Frederic WB, Murray, Jeffrey C, Wade, Claire M, Marazita, Mary L, and Bannasch, Danika L

Subjects
Brain, Animals, Dogs, Humans, Cleft Palate, Cleft Lip, Haplotypes, Frameshift Mutation, Polymorphism, Single Nucleotide, ADAM Proteins, Genome-Wide Association Study, ADAMTS Proteins, Polymorphism, Single Nucleotide, Genetics, Developmental Biology
Abstract

Cleft lip with or without cleft palate (CL/P) is the most commonly occurring craniofacial birth defect. We provide insight into the genetic etiology of this birth defect by performing genome-wide association studies in two species: dogs and humans. In the dog, a genome-wide association study of 7 CL/P cases and 112 controls from the Nova Scotia Duck Tolling Retriever (NSDTR) breed identified a significantly associated region on canine chromosome 27 (unadjusted p=1.1 x 10(-13); adjusted p= 2.2 x 10(-3)). Further analysis in NSDTR families and additional full sibling cases identified a 1.44 Mb homozygous haplotype (chromosome 27: 9.29 - 10.73 Mb) segregating with a more complex phenotype of cleft lip, cleft palate, and syndactyly (CLPS) in 13 cases. Whole-genome sequencing of 3 CLPS cases and 4 controls at 15X coverage led to the discovery of a frameshift mutation within ADAMTS20 (c.1360_1361delAA (p.Lys453Ilefs*3)), which segregated concordant with the phenotype. In a parallel study in humans, a family-based association analysis (DFAM) of 125 CL/P cases, 420 unaffected relatives, and 392 controls from a Guatemalan cohort, identified a suggestive association (rs10785430; p =2.67 x 10-6) with the same gene, ADAMTS20. Sequencing of cases from the Guatemalan cohort was unable to identify a causative mutation within the coding region of ADAMTS20, but four coding variants were found in additional cases of CL/P. In summary, this study provides genetic evidence for a role of ADAMTS20 in CL/P development in dogs and as a candidate gene for CL/P development in humans.

Published
2015

6. A LINE-1 insertion in DLX6 is responsible for cleft palate and mandibular abnormalities in a canine model of Pierre Robin sequence.

Author

Wolf, Zena T, Leslie, Elizabeth J, Arzi, Boaz, Jayashankar, Kartika, Karmi, Nili, Jia, Zhonglin, Rowland, Douglas J, Young, Amy, Safra, Noa, Sliskovic, Saundra, Murray, Jeffrey C, Wade, Claire M, and Bannasch, Danika L

Subjects
Mandible, Animals, Dogs, Humans, Cleft Palate, Pierre Robin Syndrome, Homeodomain Proteins, Long Interspersed Nucleotide Elements, Gene Frequency, Phenotype, Mutation, Missense, Polymorphism, Single Nucleotide, Genes, Homeobox, Genome-Wide Association Study, Genes, Homeobox, Mutation, Missense, Polymorphism, Single Nucleotide, Genetics, Developmental Biology
Abstract

Cleft palate (CP) is one of the most commonly occurring craniofacial birth defects in humans. In order to study cleft palate in a naturally occurring model system, we utilized the Nova Scotia Duck Tolling Retriever (NSDTR) dog breed. Micro-computed tomography analysis of CP NSDTR craniofacial structures revealed that these dogs exhibit defects similar to those observed in a recognizable subgroup of humans with CP: Pierre Robin Sequence (PRS). We refer to this phenotype in NSDTRs as CP1. Individuals with PRS have a triad of birth defects: shortened mandible, posteriorly placed tongue, and cleft palate. A genome-wide association study in 14 CP NSDTRs and 72 unaffected NSDTRs identified a significantly associated region on canine chromosome 14 (24.2 Mb-29.3 Mb; p(raw )= 4.64 × 10(-15)). Sequencing of two regional candidate homeobox genes in NSDTRs, distal-less homeobox 5 (DLX5) and distal-less homeobox 6 (DLX6), identified a 2.1 kb LINE-1 insertion within DLX6 in CP1 NSDTRs. The LINE-1 insertion is predicted to insert a premature stop codon within the homeodomain of DLX6. This prompted the sequencing of DLX5 and DLX6 in a human cohort with CP, where a missense mutation within the highly conserved DLX5 homeobox of a patient with PRS was identified. This suggests the involvement of DLX5 in the development of PRS. These results demonstrate the power of the canine animal model as a genetically tractable approach to understanding naturally occurring craniofacial birth defects in humans.

Published
2014

21. Estimated breeding values for dog breeding: Pros and cons.

Author

Wade, Claire M.

Subjects
DOG breeding, CARDIOVASCULAR diseases, PHENOTYPES, GENETICS, CARDIOVASCULAR system
Abstract

Estimated breeding values (EBVs) have been widely used in animal breeding to improve complex traits since the 1970s. They have been particularly successfully applied in the dairy and swine production industries where good quality phenotypic and pedigree information is available. In the past decade, the promotion of EBVs to improve complex trait scores in dog breeding has been proposed. In particular, the use of EBVs to improve traits relating to orthopaedic health, working performance and cardiovascular disease have been promoted. To date, the availability of EBVs for dog breeding has been limited. The reasons for this are partly historical and partly practical. In Australia, the establishment of EBVs for orthopaedic traits is likely achievable in the medium term. EBVs for other traits are unlikely to be available for the foreseeable future. [ABSTRACT FROM AUTHOR]

Published
2023

25. Genome-Wide Association Analysis Reveals a SOD1 Mutation in Canine Degenerative Myelopathy That Resembles Amyotrophic Lateral Sclerosis

Author

Awano, Tomoyuki, Johnson, Gary S., Wade, Claire M., Katz, Martin L., Johnson, Gayle C., Taylor, Jeremy F., Perloski, Michele, Biagi, Tara, Baranowska, Izabella, Long, Sam, March, Philip A., Olby, Natasha J., Shelton, G. Diane, Khan, Shahnawaz, O'Brien, Dennis P., Lindblad-Toh, Kerstin, Coates, Joan R., and Womack, James E.

Published
2009
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33. Additional file 1 of Exploiting genomic synteny in Felidae: cross-species genome alignments and SNV discovery can aid conservation management

Author

Samaha, Georgina, Wade, Claire M., Mazrier, Hamutal, Grueber, Catherine E., and Haase, Bianca

Abstract

Additional file 1: Table S1. Sequencing and alignment performance for all individual samples and species pools. Cheetah_pool, tiger_pool and snowleopard_pool refer to species pools consisting of 4 multiplexed individuals each. Figure S1. Mapped and total reads across WGS samples and pools. Total number of mapped reads (black) includes singletons and pairs. Number of paired reads mapped indicated by the grey line. Tiger_zoo, snowleopard_zoo and cheetah_zoo refer to multiplexed pool samples. Figure S2. Plots of genome coverage for each sample .bam file aligned to the felCat9 reference assembly for a. cheetah, b. Sumatran tiger and c. snow leopard cohorts. On each panel, the key indicates coloured line of each sample and their sequencing depth in brackets. Table S2. Functional annotation of all fixed and within-species SNPs for each species. Table S3a. Top 20 gene ontology terms (GOterms) enriched for species-specific SNV within cheetahs. P-values were adjusted for multiple testing using Benjamini-Hochberg false discovery rate. Table S3b. Top 20 gene ontology terms (GOterms) enriched for species specific SNVs within Sumatran tigers. P-values were adjusted for multiple testing using Benjamini-Hochberg false discovery rate. Table S4. Genes under positive selection identified as those displaying elevated πNπSratios across all three species. Table S5a. Top 20 gene ontology terms (GOterms) enriched across fixed SNVs in snow leopards. P-values were adjusted for multiple testing using Benjamini-Hochberg FDR (false discovery rate). Table S5b. Top 20 gene ontology terms (GOterms) enriched across fixed SNVs in Sumatran tigers. P-values were adjusted for multiple testing using Benjamini-Hochberg FDR (false discovery rate). Table S6. Multi-species alignment of LCORL (ENSFCAG00000029474) revealed Panthera-specific conservation of six missense variants. Cheetah, snow leopard and Sumatran tiger refer to samples aligned to the domestic cat (felCat9) reference assembly. Protein positions are reported relative to the Ensembl transcript ENSFCAT00000081895.1. Table S7. Protocadherin genes containing fixed non-synonymous SNVs common to all big cat species relative to the domestic cat (felCat9) reference assembly. Table S8. Genes containing deleterious SNVs implicated in heritable conditions affecting big cats grouped by species. Figure S3a. Gene ontology annotation of clinically significant GOterms in cheetahs. Deleterious variants were observed in 201 genes included in custom list of GO terms relevant to known heritable conditions, immune and reproductive function. These genes were annotated for terms relevant to reproductive and immune function. Network interaction graph produced by GOnet ( https://tools.dice-database.org/GOnet/ ). Figure S3b. Gene ontology annotation of clinically significant GOterms in Sumatran tigers. Deleterious variants were observed in 44 genes included in custom list of GO terms relevant to known heritable conditions, immune and reproductive function. These genes were annotated for terms relevant to cilium structure. Network interaction graph produced by GOnet ( https://tools.dice-database.org/GOnet/ ). Table S9. Samples downloaded from Sequence Read Archive (SRA) comprised six cheetahs, one snow leopard and seven Sumatran tigers. Table S10.Genes associated with size in domestic species identified from a literature search. Table S11. Selected GO enrichment terms used to classify deleterious variants potentially implicated in reproductive success and overall health of captive bred big cats. Table S12. Known heritable conditions affecting captive bred big cat species and relevant GO terms.

Published
2021
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36. Fine mapping in 94 inbred mouse strains using a high-density haplotype resource

Author

Kirby, Andrew, Hyun Min Kang, Wade, Claire M., Cotsapas, Chris, Kostem, Emrah, Han, Buhm, Furlotte, Nick, Eun Yong Kang, Rivas, Manuel, Bogue, Molly A., Frazer, Kelly A., Johnson, Frank M., Beilharz, Erica J., Cox, David R., Eskin, Eleazar, and Daly, Mark J.

Subjects
Chromosome mapping -- Research, Genetic polymorphisms -- Research, Genetic variation -- Research, Linkage (Genetics) -- Research, Biological sciences
Published
2010

38. Identification of novel genes that mediate innate immunity using inbred mice

Author

Yang, Ivana V., Wade, Claire M., Hyun Min Kang, Alper, Scott, Rutledge, Holly, Lackford, Brad, Eskin, Eleazar, Daly, Mark J., and Schwartz, David A.

Subjects
Genetic polymorphisms -- Research, Rodents as pets -- Genetic aspects, Rodents as pets -- Research, Quantitative trait loci -- Research, RNA sequencing -- Research, Genetic transcription -- Research, Biological sciences
Published
2009

40. Efficient control of population structure in model organism association mapping

Author

Kang, Hyun Min, Zaitlen, Noah A., Wade, Claire M., Kirby, Andrew, Heckerman, David, Daly, Mark J., and Eskin, Eleazar

Subjects
Chromosome mapping -- Methods, Population genetics -- Research, Genes -- Identification and classification, Gene expression -- Research, Biological sciences
Abstract

Genomewide association mapping in model organisms such as inbred mouse strains is a promising approach for the identification of risk factors related to human diseases. However, genetic association studies in inbred model organisms are confronted by the problem of complex population structure among strains. This induces inflated false positive rates, which cannot be corrected using standard approaches applied in human association studies such as genomic control or structured association. Recent studies demonstrated that mixed models successfully correct for the genetic relatedness in association mapping in maize and Arabidopsis panel data sets. However, the currently available mixed-model methods suffer from computational inefficiency. In this article, we propose a new method, efficient mixed-model association (EMMA), which corrects for population structure and genetic relatedness in model organism association mapping. Our method takes advantage of the specific nature of the optimization problem in applying mixed models for association mapping, which allows us to substantially increase the computational speed and reliability of the results. We applied EMMA to in silico whole-genome association mapping of inbred mouse strains involving hundreds of thousands of SNPs, in addition to Arabidopsis and maize data sets. We also performed extensive simulation studies to estimate the statistical power of EMMA under various SNP effects, varying degrees of population structure, and differing numbers of multiple measurements per strain. Despite the limited power of inbred mouse association mapping due to the limited number of available inbred strains, we are able to identify significantly associated SNPs, which fall into known QTL or genes identified through previous studies while avoiding an inflation of false positives. An R package implementation and webserver of our EMMA method are publicly available.

Published
2008

41. Genome of the marsupial Monodelphis domestica reveals innovation in non-coding sequences

Author

Mikkelsen, Tarjei S., Wakefield, Matthew J., Aken, Bronwen, Amemiya, Chris T., Chang, Jean L., Duke, Shannon, Garber, Manuel, Gentles, Andrew J., Goodstadt, Leo, Heger, Andreas, Jurka, Jerzy, Kamal, Michael, Mauceli, Evan, Searle, Stephen M. J., Sharpe, Ted, Baker, Michelle L., Batzer, Mark A., Benos, Panayiotis V., Belov, Katherine, Clamp, Michele, Cook, April, Cuff, James, Das, Radhika, Davidow, Lance, Deakin, Janine E., Fazzari, Melissa J., Glass, Jacob L., Grabherr, Manfred, Greally, John M., Gu, Wanjun, Hore, Timothy A., Huttley, Gavin A., Kleber, Michael, Jirtle, Randy L., Koina, Edda, Lee, Jeannie T., Mahony, Shaun, Marra, Marco A., Miller, Robert D., Nicholls, Robert D., Oda, Mayumi, Papenfuss, Anthony T., Parra, Zuly E., Pollock, David D., Ray, David A., Schein, Jacqueline E., Speed, Terence P., Thompson, Katherine, VandeBerg, John L., Wade, Claire M., Walker, Jerilyn A., Waters, Paul D., Webber, Caleb, Weidman, Jennifer R., Xie, Xiaohui, Zody, Michael C., Baldwin, Jennifer, Abdouelleil, Amr, Abdulkadir, Jamal, Abebe, Adal, Abera, Brikti, Abreu, Justin, Acer, St Christophe, Aftuck, Lynne, Alexander, Allen, An, Peter, Anderson, Erica, Anderson, Scott, Arachi, Harindra, Azer, Marc, Bachantsang, Pasang, Barry, Andrew, Bayul, Tashi, Berlin, Aaron, Bessette, Daniel, Bloom, Toby, Blye, Jason, Boguslavskiy, Leonid, Bonnet, Claude, Boukhgalter, Boris, Bourzgui, Imane, Brown, Adam, Cahill, Patrick, Channer, Sheridon, Cheshatsang, Yama, Chuda, Lisa, Citroen, Mieke, Collymore, Alville, Cooke, Patrick, Costello, Maura, D'Aco, Katie, Daza, Riza, De Haan, Georgius, DeGray, Stuart, DeMaso, Christina, Dhargay, Norbu, Dooley, Kimberly, Dooley, Erin, Doricent, Missole, Dorje, Passang, Dorjee, Kunsang, Dupes, Alan, Elong, Richard, Falk, Jill, Farina, Abderrahim, Faro, Susan, Ferguson, Diallo, Fisher, Sheila, Foley, Chelsea D., Franke, Alicia, Friedrich, Dennis, Gadbois, Loryn, Gearin, Gary, Gearin, Christina R., Giannoukos, Georgia, Goode, Tina, Graham, Joseph, Grandbois, Edward, Grewal, Sharleen, Gyaltsen, Kunsang, Hafez, Nabil, Hagos, Birhane, Hall, Jennifer, Henson, Charlotte, Hollinger, Andrew, Honan, Tracey, Huard, Monika D., Hughes, Leanne, Hurhula, Brian, Husby, M. Erii, Kamat, Asha, Kanga, Ben, Kashin, Seva, Khazanovich, Dmitry, Kisner, Peter, Lance, Krista, Lara, Marcia, Lee, William, Lennon, Niall, Letendre, Frances, LeVine, Rosie, Lipovsky, Alex, Liu, Xiaohong, Liu, Jinlei, Liu, Shangtao, Lokyitsang, Tashi, Lokyitsang, Yeshi, Lubonja, Rakela, Lui, Annie, MacDonald, Pen, Magnisalis, Vasilia, Maru, Kebede, Matthews, Charles, McCusker, William, McDonough, Susan, Mehta, Teena, Meldrim, James, Meneus, Louis, Mihai, Oana, Mihalev, Atanas, Mihova, Tanya, Mittelman, Rachel, Mlenga, Valentine, Montmayeur, Anna, Mulrain, Leonidas, Navidi, Adam, Naylor, Jerome, Negash, Tamrat, Nguyen, Thu, Nguyen, Nga, Nicol, Robert, Norbu, Choe, Norbu, Nyima, Novod, Nathaniel, O'Neill, Barry, Osman, Sahal, Markiewicz, Eva, Oyono, Otero L., Patti, Christopher, Phunkhang, Pema, Pierre, Fritz, Priest, Margaret, Raghuraman, Sujaa, Rege, Filip, Reyes, Rebecca, Rise, Cecil, Rogov, Peter, Ross, Keenan, Ryan, Elizabeth, Settipalli, Sampath, Shea, Terry, Sherpa, Ngawang, Shi, Lu, Shih, Diana, Sparrow, Todd, Spaulding, Jessica, Stalker, John, Stange-Thomann, Nicole, Stavropoulos, Sharon, Stone, Catherine, Strader, Christopher, Tesfaye, Senait, Thomson, Talene, Thoulutsang, Yama, Thoulutsang, Dawa, Topham, Kerri, Topping, Ira, Tsamla, Tsamla, Vassiliev, Helen, Vo, Andy, Wangchuk, Tsering, Wangdi, Tsering, Weiand, Michael, Wilkinson, Jane, Wilson, Adam, Yadav, Shailendra, Young, Geneva, Yu, Qing, Zembek, Lisa, Zhong, Danni, Zimmer, Andrew, Zwirko, Zac, Jaffe, David B., Alvarez, Pablo, Brockman, Will, Butler, Jonathan, Chin, CheeWhye, Gnerre, Sante, MacCallum, Iain, Graves, Jennifer A. Marshall, Ponting, Chris P., Breen, Matthew, Samollow, Paul B., Lander, Eric S., and Lindblad-Toh, Kerstin

Subjects
Environmental issues, Science and technology, Zoology and wildlife conservation
Abstract

Author(s): Tarjei S. Mikkelsen (corresponding author) [1, 2]; Matthew J. Wakefield [3]; Bronwen Aken [4]; Chris T. Amemiya [5]; Jean L. Chang [1]; Shannon Duke [6]; Manuel Garber [1]; Andrew [...]

Published
2007
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42. Insights from the genome of the biotrophic fungal plant pathogen Ustilago maydis

Author

Kamper, Jorg, Kahmann, Regine, Bolker, Michael, Ma, Li-Jun, Brefort, Thomas, Saville, Barry J., Banuett, Flora, Kronstad, James W., Gold, Scott E., Muller, Olaf, Perlin, Michael H., Wosten, Han A. B., de Vries, Ronald, Ruiz-Herrera, Jose, Reynaga-Pena, Cristina G., Snetselaar, Karen, McCann, Michael, Perez-Martin, Jose, Feldbrugge, Michael, Basse, Christoph W., Steinberg, Gero, Ibeas, Jose I., Holloman, William, Guzman, Plinio, Farman, Mark, Stajich, Jason E., Sentandreu, Rafael, Gonzalez-Prieto, Juan M., Kennell, John C., Molina, Lazaro, Schirawski, Jan, Mendoza-Mendoza, Artemio, Greilinger, Doris, Munch, Karin, Rossel, Nicole, Scherer, Mario, Vraneš, Miroslav, Ladendorf, Oliver, Vincon, Volker, Fuchs, Uta, Sandrock, Bjorn, Meng, Shaowu, Ho, Eric C. H., Cahill, Matt J., Boyce, Kylie J., Klose, Jana, Klosterman, Steven J., Deelstra, Heine J., Ortiz-Castellanos, Lucila, Li, Weixi, Sanchez-Alonso, Patricia, Schreier, Peter H., Hauser-Hahn, Isolde, Vaupel, Martin, Koopmann, Edda, Friedrich, Gabi, Voss, Hartmut, Schluter, Thomas, Margolis, Jonathan, Platt, Darren, Swimmer, Candace, Gnirke, Andreas, Chen, Feng, Vysotskaia, Valentina, Mannhaupt, Gertrud, Guldener, Ulrich, Munsterkotter, Martin, Haase, Dirk, Oesterheld, Matthias, Mewes, Hans-Werner, Mauceli, Evan W., DeCaprio, David, Wade, Claire M., Butler, Jonathan, Young, Sarah, Jaffe, David B., Calvo, Sarah, Nusbaum, Chad, Galagan, James, and Birren, Bruce W.

Abstract

Author(s): Jörg Kämper (corresponding author) [1]; Regine Kahmann (corresponding author) [1]; Michael Bölker (corresponding author) [2]; Li-Jun Ma [3]; Thomas Brefort [1]; Barry J. Saville [4, 27]; Flora Banuett [5]; [...]

Published
2006
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43. Genome sequence, comparative analysis and haplotype structure of the domestic dog

Author

Lindblad-Toh, Kerstin, Wade, Claire M., Mikkelsen, Tarjei S., Karlsson, Elinor K., Jaffe, David B., Kamal, Michael, Clamp, Michele, Chang, Jean L., Kulbokas, III, Edward J., Zody, Michael C., Mauceli, Evan, Xie, Xiaohui, Breen, Matthew, Wayne, Robert K., Ostrander, Elaine A., Ponting, Chris P., Galibert, Francis, Smith, Douglas R., deJong, Pieter J., Kirkness, Ewen, Alvarez, Pablo, Biagi, Tara, Brockman, William, Butler, Jonathan, Chin, Chee-Wye, Cook, April, Cuff, James, Daly, Mark J., DeCaprio, David, Gnerre, Sante, Grabherr, Manfred, Kellis, Manolis, Kleber, Michael, Bardeleben, Carolyne, Goodstadt, Leo, Heger, Andreas, Hitte, Christophe, Kim, Lisa, Koepfli, Klaus-Peter, Parker, Heidi G., Pollinger, John P., Searle, Stephen M. J., Sutter, Nathan B., Thomas, Rachael, Webber, Caleb, Baldwin, Jennifer, Abebe, Adal, Abouelleil, Amr, Aftuck, Lynne, Ait-zahra, Mostafa, Aldredge, Tyler, Allen, Nicole, An, Peter, Anderson, Scott, Antoine, Claudel, Arachchi, Harindra, Aslam, Ali, Ayotte, Laura, Bachantsang, Pasang, Barry, Andrew, Bayul, Tashi, Benamara, Mostafa, Berlin, Aaron, Bessette, Daniel, Blitshteyn, Berta, Bloom, Toby, Blye, Jason, Boguslavskiy, Leonid, Bonnet, Claude, Boukhgalter, Boris, Brown, Adam, Cahill, Patrick, Calixte, Nadia, Camarata, Jody, Cheshatsang, Yama, Chu, Jeffrey, Citroen, Mieke, Collymore, Alville, Cooke, Patrick, Dawoe, Tenzin, Daza, Riza, Decktor, Karin, DeGray, Stuart, Dhargay, Norbu, Dooley, Kimberly, Dooley, Kathleen, Dorje, Passang, Dorjee, Kunsang, Dorris, Lester, Duffey, Noah, Dupes, Alan, Egbiremolen, Osebhajajeme, Elong, Richard, Falk, Jill, Farina, Abderrahim, Faro, Susan, Ferguson, Diallo, Ferreira, Patricia, Fisher, Sheila, FitzGerald, Mike, Foley, Karen, Foley, Chelsea, Franke, Alicia, Friedrich, Dennis, Gage, Diane, Garber, Manuel, Gearin, Gary, Giannoukos, Georgia, Goode, Tina, Goyette, Audra, Graham, Joseph, Grandbois, Edward, Gyaltsen, Kunsang, Hafez, Nabil, Hagopian, Daniel, Hagos, Birhane, Hall, Jennifer, Healy, Claire, Hegarty, Ryan, Honan, Tracey, Horn, Andrea, Houde, Nathan, Hughes, Leanne, Hunnicutt, Leigh, Husby, M., Jester, Benjamin, Jones, Charlien, Kamat, Asha, Kanga, Ben, Kells, Cristyn, Khazanovich, Dmitry, Kieu, Alix Chinh, Kisner, Peter, Kumar, Mayank, Lance, Krista, Landers, Thomas, Lara, Marcia, Lee, William, Leger, Jean-Pierre, Lennon, Niall, Leuper, Lisa, LeVine, Sarah, Liu, Jinlei, Liu, Xiaohong, Lokyitsang, Yeshi, Lokyitsang, Tashi, Lui, Annie, Macdonald, Jan, Major, John, Marabella, Richard, Maru, Kebede, Matthews, Charles, McDonough, Susan, Mehta, Teena, Meldrim, James, Melnikov, Alexandre, Meneus, Louis, Mihalev, Atanas, Mihova, Tanya, Miller, Karen, Mittelman, Rachel, Mlenga, Valentine, Mulrain, Leonidas, Munson, Glen, Navidi, Adam, Naylor, Jerome, Nguyen, Tuyen, Nguyen, Nga, Nguyen, Cindy, Nguyen, Thu, Nicol, Robert, Norbu, Nyima, Norbu, Choe, Novod, Nathaniel, Nyima, Tenchoe, Olandt, Peter, O'Neill, Barry, O'Neill, Keith, Osman, Sahal, Oyono, Lucien, Patti, Christopher, Perrin, Danielle, Phunkhang, Pema, Pierre, Fritz, Priest, Margaret, Rachupka, Anthony, Raghuraman, Sujaa, Rameau, Rayale, Ray, Verneda, Raymond, Christina, Rege, Filip, Rise, Cecil, Rogers, Julie, Rogov, Peter, Sahalie, Julie, Settipalli, Sampath, Sharpe, Theodore, Shea, Terrance, Sheehan, Mechele, Sherpa, Ngawang, Shi, Jianying, Shih, Diana, Sloan, Jessie, Smith, Cherylyn, Sparrow, Todd, Stalker, John, Stange-Thomann, Nicole, Stavropoulos, Sharon, Stone, Catherine, Stone, Sabrina, Sykes, Sean, Tchuinga, Pierre, Tenzing, Pema, Tesfaye, Senait, Thoulutsang, Dawa, Thoulutsang, Yama, Topham, Kerri, Topping, Ira, Tsamla, Tsamla, Vassiliev, Helen, Venkataraman, Vijay, Vo, Andy, Wangchuk, Tsering, Wangdi, Tsering, Weiand, Michael, Wilkinson, Jane, Wilson, Adam, Yadav, Shailendra, Yang, Shuli, Yang, Xiaoping, Young, Geneva, Yu, Qing, Zainoun, Joanne, Zembek, Lisa, Zimmer, Andrew, and Lander, Eric S.

Subjects
Environmental issues, Science and technology, Zoology and wildlife conservation
Abstract

Author(s): Kerstin Lindblad-Toh (corresponding author) [1]; Claire M Wade [1, 2]; Tarjei S. Mikkelsen [1, 3]; Elinor K. Karlsson [1, 4]; David B. Jaffe [1]; Michael Kamal [1]; Michele Clamp [...]

Published
2005
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44. Forensic DNA phenotyping: Canis familiaris breed classification and skeletal phenotype prediction using functionally significant skeletal SNPs and indels.

Author

Raymond, Patrick W., Velie, Brandon D., and Wade, Claire M.

Subjects
CANIS, DNA, DOGS, SINGLE nucleotide polymorphisms, GENETIC variation, TANDEM repeats
Abstract

Summary: This review highlights a novel application of breed identification and prediction of skeletal traits in forensic investigations using canine DNA evidence. Currently, genotyping methods used for canine breed classification involve the application of highly polymorphic short tandem repeats in addition to larger commercially available SNP arrays. Both applications face technical challenges. An additional approach to breed identification could be through genotyping SNPs and indels that characterise the array of skeletal differences displayed across domestic dog populations. Research has shown that a small number of genetic variants of large effect drive differences in skeletal phenotypes among domestic dog breeds. This feature makes functionally significant canine skeletal variants a cost‐effective target for forensic investigators to classify individuals according to their breed. Further analysis of these skeletal variants would enable the prediction of external appearance. To date, functionally significant genes with genetic variants associated with differences in size, bulk, skull shape, ear shape, limb length, digit type, and tail morphology have been uncovered. Recommendations of a cost‐effective genotyping method that can be readily designed and applied by forensic investigators have been given. Further advances to improve the field of canine skeletal forensic DNA phenotyping include the refinement of phenotyping methods, further biological validation of the skeletal genetic variants and establishing a publicly available database for storage of allele frequencies of the skeletal genetic variants in the wider domestic dog population. [ABSTRACT FROM AUTHOR]

Published
2022
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45. Initial sequencing and comparative analysis of the mouse genome

Author

Chinwalla, Asif T., Cook, Lisa L., Delehaunty, Kimberly D., Fewell, Ginger A., Fulton, Lucinda A., Fulton, Robert S., Graves, Tina A., Hillier, LaDeana W., Mardis, Elaine R., McPherson, John D., Miner, Tracie L., Nash, William E., Nelson, Joanne O., Nhan, Michael N., Pepin, Kymberlie H., Pohl, Craig S., Ponce, Tracy C., Schultz, Brian, Thompson, Johanna, Trevaskis, Evanne, Waterston, Robert H., Wendl, Michael C., Wilson, Richard K., Yang, Shiaw-Pyng, An, Peter, Berry, Eric, Birren, Bruce, Bloom, Toby, Brown, Daniel G., Butler, Jonathan, Daly, Mark, David, Robert, Deri, Justin, Dodge, Sheila, Foley, Karen, Gage, Diane, Gnerre, Sante, Holzer, Timothy, Jaffe, David B., Kamal, Michael, Karlsson, Elinor K., Kells, Cristyn, Kirby, Andrew, Kulbokas, III, Edward J., Lander, Eric S., Landers, Tom, Leger, J. P., Levine, Rosie, Lindblad-Toh, Kerstin, Mauceli, Evan, Mayer, John H., McCarthy, Megan, Meldrim, Jim, Mesirov, Jill P., Nicol, Robert, Nusbaum, Chad, Seaman, Steven, Sharpe, Ted, Sheridan, Andrew, Singer, Jonathan B., Santos, Ralph, Spencer, Brian, Stange-Thomann, Nicole, Vinson, Jade P., Wade, Claire M., Wierzbowski, Jamey, Wyman, Dudley, Zody, Michael C., Birney, Ewan, Goldman, Nick, Kasprzyk, Arkadiusz, Mongin, Emmanuel, Rust, Alistair G., Slater, Guy, Stabenau, Arne, Ureta-Vidal, Abel, Whelan, Simon, Ainscough, Rachel, Attwood, John, Bailey, Jonathon, Barlow, Karen, Beck, Stephan, Burton, John, Clamp, Michele, Clee, Christopher, Coulson, Alan, Cuff, James, Curwen, Val, Cutts, Tim, Davies, Joy, Eyras, Eduardo, Grafham, Darren, Gregory, Simon, Hubbard, Tim, Hunt, Adrienne, Jones, Matthew, Joy, Ann, Leonard, Steven, Lloyd, Christine, Matthews, Lucy, McLaren, Stuart, McLay, Kirsten, Meredith, Beverley, Mullikin, James C., Ning, Zemin, Oliver, Karen, Overton-Larty, Emma, Plumb, Robert, Potter, Simon, Quail, Michael, Rogers, Jane, Scott, Carol, Searle, Steve, Shownkeen, Ratna, Sims, Sarah, Wall, Melanie, West, Anthony P., Willey, David, Williams, Sophie, Abril, Josep F., Guigo, Roderic, Parra, Genis, Agarwal, Pankaj, Agarwala, Richa, Church, Deanna M., Hlavina, Wratko, Maglott, Donna R., Sapojnikov, Victor, Alexandersson, Marina, Pachter, Lior, Antonarakis, Stylianos E., Dermitzakis, Emmanouil T., Reymond, Alexandre, Ucla, Catherine, Baertsch, Robert, Diekhans, Mark, Furey, Terrence S., Hinrichs, Angela, Hsu, Fan, Karolchik, Donna, Kent, W. James, Roskin, Krishna M., Schwartz, Matthias S., Sugnet, Charles, Weber, Ryan J., Bork, Peer, Letunic, Ivica, Suyama, Mikita, Torrents, David, Zdobnov, Evgeny M., Botcherby, Marc, Brown, Stephen D., Campbell, Robert D., Jackson, Ian, Bray, Nicolas, Couronne, Olivier, Dubchak, Inna, Poliakov, Alex, Rubin, Edward M., Brent, Michael R., Flicek, Paul, Keibler, Evan, Korf, Ian, Batalov, S., Bult, Carol, Frankel, Wayne N., Carninci, Piero, Hayashizaki, Yoshihide, Kawai, Jun, Okazaki, Yasushi, Cawley, Simon, Kulp, David, Wheeler, Raymond, Chiaromonte, Francesca, Collins, Francis S., Felsenfeld, Adam, Guyer, Mark, Peterson, Jane, Wetterstrand, Kris, Copley, Richard R., Mott, Richard, Dewey, Colin, Dickens, Nicholas J., Emes, Richard D., Goodstadt, Leo, Ponting, Chris P., Winter, Eitan, Dunn, Diane M., von Niederhausern, Andrew C., Weiss, Robert B., Eddy, Sean R., Johnson, L. Steven, Jones, Thomas A., Elnitski, Laura, Kolbe, Diana L., Eswara, Pallavi, Miller, Webb, O'Connor, Michael J., Schwartz, Scott, Muzny, Donna M., Glusman, Gustavo, Smit, Arian, Green, Eric D., Hardison, Ross C., Yang, Shan, Haussler, David, Hua, Axin, Roe, Bruce A., Kucherlapati, Raju S., Montgomery, Kate T., Li, Jia, Li, Ming, Lucas, Susan, Ma, Bin, McCombie, W. Richard, Morgan, Michael, Pevzner, Pavel, Tesler, Glenn, Schultz, Jorg, Smith, Douglas R., Tromp, John, and Worley, Kim C.

Subjects
Environmental issues, Science and technology, Zoology and wildlife conservation
Abstract

Author(s): Mouse Genome Sequencing Consortium ; Genome Sequencing Center: ; Asif T. Chinwalla [1, 47]; Lisa L. Cook [1]; Kimberly D. Delehaunty [1]; Ginger A. Fewell [1]; Lucinda A. Fulton [...]

Published
2002
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46. The mosaic structure of variation in the laboratory mouse genome

Author

Wade, Claire M., Kulbokas, III, Edward J., Kirby, Andrew W., Zody, Michael C., Mullikin, James C., Lander, Eric S., Lindblad-Toh, Kerstin, and Daly, Mark J.

Subjects
Environmental issues, Science and technology, Zoology and wildlife conservation
Abstract

Author(s): Claire M. Wade [1, 2]; Edward J. Kulbokas, III [1]; Andrew W. Kirby [1]; Michael C. Zody [1]; James C. Mullikin [3]; Eric S. Lander [1]; Kerstin Lindblad-Toh [1, [...]

Published
2002
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