Generation of an equine biobank to be used for Functional Annotation of Animal Genomes project

E. N. Burns, M. H. Bordbari, M. J. Mienaltowski, V. K. Affolter, M. V. Barro, F. Gianino, G. Gianino, E. Giulotto, T. S. Kalbfleisch, S. A. Katzman, M. Lassaline, T. Leeb, M. Mack, E. J. Müller, J. N. MacLeod, B. Ming-Whitfield, C. R. Alanis, T. Raudsepp, E. Scott, S. VigH. Zhou, J. L. Petersen, R. R. Bellone, C. J. Finno

Research output: Contribution to journalArticle

2 Citations (Scopus)

Abstract

The Functional Annotation of Animal Genomes (FAANG) project aims to identify genomic regulatory elements in both sexes across multiple stages of development in domesticated animals. This study represents the first stage of the FAANG project for the horse, Equus caballus. A biobank of 80 tissue samples, two cell lines and six body fluids was created from two adult Thoroughbred mares. Ante-mortem assessments included full physical examinations, lameness, ophthalmologic and neurologic evaluations. Complete blood counts and serum biochemistries were also performed. At necropsy, in addition to tissue samples, aliquots of serum, ethylenediaminetetraacetic acid (EDTA) plasma, heparinized plasma, cerebrospinal fluid, synovial fluid, urine and microbiome samples from all regions of the gastrointestinal and urogenital tracts were collected. Epidermal keratinocytes and dermal fibroblasts were cultured from skin samples. All tissues were grossly and histologically evaluated by a board-certified veterinary pathologist. The results of the clinical and pathological evaluations identified subclinical eosinophilic and lymphocytic infiltration throughout the length of the gastrointestinal tract as well as a mild clinical lameness in both animals. Each sample was cryo-preserved in multiple ways, and nuclei were extracted from selected tissues. These samples represent the first published systemically healthy equine-specific biobank with extensive clinical phenotyping ante- and post-mortem. The tissues in the biobank are intended for community-wide use in the functional annotation of the equine genome. The use of the biobank will improve the quality of the reference annotation and allow all equine researchers to elucidate unknown genomic and epigenomic causes of disease.

Original languageEnglish (US)
Pages (from-to)564-570
Number of pages7
JournalAnimal genetics
Volume49
Issue number6
DOIs
StatePublished - Dec 2018

Fingerprint

Horses
Genome
horses
genome
animals
Gastrointestinal Tract
blood serum
sampling
lameness
Skin
Blood Cell Count
Synovial Fluid
Microbiota
Domestic Animals
genomics
Body Fluids
synovial fluid
Serum
Keratinocytes
Epigenomics

Keywords

  • biorepository
  • genome regulation
  • horse
  • necropsy
  • nuclei isolation
  • tissue collection

ASJC Scopus subject areas

  • Animal Science and Zoology
  • Genetics

Cite this

Burns, E. N., Bordbari, M. H., Mienaltowski, M. J., Affolter, V. K., Barro, M. V., Gianino, F., ... Finno, C. J. (2018). Generation of an equine biobank to be used for Functional Annotation of Animal Genomes project. Animal genetics, 49(6), 564-570. https://doi.org/10.1111/age.12717

Generation of an equine biobank to be used for Functional Annotation of Animal Genomes project. / Burns, E. N.; Bordbari, M. H.; Mienaltowski, M. J.; Affolter, V. K.; Barro, M. V.; Gianino, F.; Gianino, G.; Giulotto, E.; Kalbfleisch, T. S.; Katzman, S. A.; Lassaline, M.; Leeb, T.; Mack, M.; Müller, E. J.; MacLeod, J. N.; Ming-Whitfield, B.; Alanis, C. R.; Raudsepp, T.; Scott, E.; Vig, S.; Zhou, H.; Petersen, J. L.; Bellone, R. R.; Finno, C. J.

In: Animal genetics, Vol. 49, No. 6, 12.2018, p. 564-570.

Research output: Contribution to journalArticle

Burns, EN, Bordbari, MH, Mienaltowski, MJ, Affolter, VK, Barro, MV, Gianino, F, Gianino, G, Giulotto, E, Kalbfleisch, TS, Katzman, SA, Lassaline, M, Leeb, T, Mack, M, Müller, EJ, MacLeod, JN, Ming-Whitfield, B, Alanis, CR, Raudsepp, T, Scott, E, Vig, S, Zhou, H, Petersen, JL, Bellone, RR & Finno, CJ 2018, 'Generation of an equine biobank to be used for Functional Annotation of Animal Genomes project', Animal genetics, vol. 49, no. 6, pp. 564-570. https://doi.org/10.1111/age.12717
Burns EN, Bordbari MH, Mienaltowski MJ, Affolter VK, Barro MV, Gianino F et al. Generation of an equine biobank to be used for Functional Annotation of Animal Genomes project. Animal genetics. 2018 Dec;49(6):564-570. https://doi.org/10.1111/age.12717
Burns, E. N. ; Bordbari, M. H. ; Mienaltowski, M. J. ; Affolter, V. K. ; Barro, M. V. ; Gianino, F. ; Gianino, G. ; Giulotto, E. ; Kalbfleisch, T. S. ; Katzman, S. A. ; Lassaline, M. ; Leeb, T. ; Mack, M. ; Müller, E. J. ; MacLeod, J. N. ; Ming-Whitfield, B. ; Alanis, C. R. ; Raudsepp, T. ; Scott, E. ; Vig, S. ; Zhou, H. ; Petersen, J. L. ; Bellone, R. R. ; Finno, C. J. / Generation of an equine biobank to be used for Functional Annotation of Animal Genomes project. In: Animal genetics. 2018 ; Vol. 49, No. 6. pp. 564-570.
@article{a41055a1f5e44129a65e8ebc23643e08,
title = "Generation of an equine biobank to be used for Functional Annotation of Animal Genomes project",
abstract = "The Functional Annotation of Animal Genomes (FAANG) project aims to identify genomic regulatory elements in both sexes across multiple stages of development in domesticated animals. This study represents the first stage of the FAANG project for the horse, Equus caballus. A biobank of 80 tissue samples, two cell lines and six body fluids was created from two adult Thoroughbred mares. Ante-mortem assessments included full physical examinations, lameness, ophthalmologic and neurologic evaluations. Complete blood counts and serum biochemistries were also performed. At necropsy, in addition to tissue samples, aliquots of serum, ethylenediaminetetraacetic acid (EDTA) plasma, heparinized plasma, cerebrospinal fluid, synovial fluid, urine and microbiome samples from all regions of the gastrointestinal and urogenital tracts were collected. Epidermal keratinocytes and dermal fibroblasts were cultured from skin samples. All tissues were grossly and histologically evaluated by a board-certified veterinary pathologist. The results of the clinical and pathological evaluations identified subclinical eosinophilic and lymphocytic infiltration throughout the length of the gastrointestinal tract as well as a mild clinical lameness in both animals. Each sample was cryo-preserved in multiple ways, and nuclei were extracted from selected tissues. These samples represent the first published systemically healthy equine-specific biobank with extensive clinical phenotyping ante- and post-mortem. The tissues in the biobank are intended for community-wide use in the functional annotation of the equine genome. The use of the biobank will improve the quality of the reference annotation and allow all equine researchers to elucidate unknown genomic and epigenomic causes of disease.",
keywords = "biorepository, genome regulation, horse, necropsy, nuclei isolation, tissue collection",
author = "Burns, {E. N.} and Bordbari, {M. H.} and Mienaltowski, {M. J.} and Affolter, {V. K.} and Barro, {M. V.} and F. Gianino and G. Gianino and E. Giulotto and Kalbfleisch, {T. S.} and Katzman, {S. A.} and M. Lassaline and T. Leeb and M. Mack and M{\"u}ller, {E. J.} and MacLeod, {J. N.} and B. Ming-Whitfield and Alanis, {C. R.} and T. Raudsepp and E. Scott and S. Vig and H. Zhou and Petersen, {J. L.} and Bellone, {R. R.} and Finno, {C. J.}",
year = "2018",
month = "12",
doi = "10.1111/age.12717",
language = "English (US)",
volume = "49",
pages = "564--570",
journal = "Animal Genetics",
issn = "0268-9146",
publisher = "Wiley-Blackwell",
number = "6",

}

TY - JOUR

T1 - Generation of an equine biobank to be used for Functional Annotation of Animal Genomes project

AU - Burns, E. N.

AU - Bordbari, M. H.

AU - Mienaltowski, M. J.

AU - Affolter, V. K.

AU - Barro, M. V.

AU - Gianino, F.

AU - Gianino, G.

AU - Giulotto, E.

AU - Kalbfleisch, T. S.

AU - Katzman, S. A.

AU - Lassaline, M.

AU - Leeb, T.

AU - Mack, M.

AU - Müller, E. J.

AU - MacLeod, J. N.

AU - Ming-Whitfield, B.

AU - Alanis, C. R.

AU - Raudsepp, T.

AU - Scott, E.

AU - Vig, S.

AU - Zhou, H.

AU - Petersen, J. L.

AU - Bellone, R. R.

AU - Finno, C. J.

PY - 2018/12

Y1 - 2018/12

N2 - The Functional Annotation of Animal Genomes (FAANG) project aims to identify genomic regulatory elements in both sexes across multiple stages of development in domesticated animals. This study represents the first stage of the FAANG project for the horse, Equus caballus. A biobank of 80 tissue samples, two cell lines and six body fluids was created from two adult Thoroughbred mares. Ante-mortem assessments included full physical examinations, lameness, ophthalmologic and neurologic evaluations. Complete blood counts and serum biochemistries were also performed. At necropsy, in addition to tissue samples, aliquots of serum, ethylenediaminetetraacetic acid (EDTA) plasma, heparinized plasma, cerebrospinal fluid, synovial fluid, urine and microbiome samples from all regions of the gastrointestinal and urogenital tracts were collected. Epidermal keratinocytes and dermal fibroblasts were cultured from skin samples. All tissues were grossly and histologically evaluated by a board-certified veterinary pathologist. The results of the clinical and pathological evaluations identified subclinical eosinophilic and lymphocytic infiltration throughout the length of the gastrointestinal tract as well as a mild clinical lameness in both animals. Each sample was cryo-preserved in multiple ways, and nuclei were extracted from selected tissues. These samples represent the first published systemically healthy equine-specific biobank with extensive clinical phenotyping ante- and post-mortem. The tissues in the biobank are intended for community-wide use in the functional annotation of the equine genome. The use of the biobank will improve the quality of the reference annotation and allow all equine researchers to elucidate unknown genomic and epigenomic causes of disease.

AB - The Functional Annotation of Animal Genomes (FAANG) project aims to identify genomic regulatory elements in both sexes across multiple stages of development in domesticated animals. This study represents the first stage of the FAANG project for the horse, Equus caballus. A biobank of 80 tissue samples, two cell lines and six body fluids was created from two adult Thoroughbred mares. Ante-mortem assessments included full physical examinations, lameness, ophthalmologic and neurologic evaluations. Complete blood counts and serum biochemistries were also performed. At necropsy, in addition to tissue samples, aliquots of serum, ethylenediaminetetraacetic acid (EDTA) plasma, heparinized plasma, cerebrospinal fluid, synovial fluid, urine and microbiome samples from all regions of the gastrointestinal and urogenital tracts were collected. Epidermal keratinocytes and dermal fibroblasts were cultured from skin samples. All tissues were grossly and histologically evaluated by a board-certified veterinary pathologist. The results of the clinical and pathological evaluations identified subclinical eosinophilic and lymphocytic infiltration throughout the length of the gastrointestinal tract as well as a mild clinical lameness in both animals. Each sample was cryo-preserved in multiple ways, and nuclei were extracted from selected tissues. These samples represent the first published systemically healthy equine-specific biobank with extensive clinical phenotyping ante- and post-mortem. The tissues in the biobank are intended for community-wide use in the functional annotation of the equine genome. The use of the biobank will improve the quality of the reference annotation and allow all equine researchers to elucidate unknown genomic and epigenomic causes of disease.

KW - biorepository

KW - genome regulation

KW - horse

KW - necropsy

KW - nuclei isolation

KW - tissue collection

UR - http://www.scopus.com/inward/record.url?scp=85054764459&partnerID=8YFLogxK

UR - http://www.scopus.com/inward/citedby.url?scp=85054764459&partnerID=8YFLogxK

U2 - 10.1111/age.12717

DO - 10.1111/age.12717

M3 - Article

C2 - 30311254

AN - SCOPUS:85054764459

VL - 49

SP - 564

EP - 570

JO - Animal Genetics

JF - Animal Genetics

SN - 0268-9146

IS - 6

ER -