First genome-wide CNV mapping in FELIS CATUS using next generation sequencing data

F. Genova; M. Longeri; L. A. Lyons; A. Bagnato; Barbara Gandolfi; Danielle Aberdein; Paulo C. Alves; Gregory S. Barsh; Holly C. Beale; Tomas F. Bergström; Adam R. Boyko; Jeffrey A. Brockman; Marta G. Castelhano; Patricia P. Chan; Brian W. Davis; Ottmar Distl; Nicholas H. Dodman; N. Matthew Ellinwood; Jonathan E. Fogle; Oliver P. Forman; Dorian J. Garrick; Jens Häggström; Christopher R. Helps; Marjo K. Hytönen; Daniel M. Ibrahim; Maria Kaukonen; Christopher B. Kaelin; Emilie Leclerc; Teri L. Lear; Tosso Leeb; Hannes Lohi; Darío G. Lupiáñez; Mark A. Magnuson; Richard Malik; Michael J. Montague; John S. Munday; William J. Murphy; Elaine A. Ostrander; Niels C. Pedersen; Simon M. Petersen-Jones; Max F. Rothschild; Beth Shapiro; Joshua A. Stern; William F. Swanson; Karen A. Terio; Rory J. Todhunter; Yu Ueda; Wesley C. Warren; Elizabeth A. Wilcox; Julia H. Wildschutte; Edward I. Ginns; M. G. Strillacci

doi:10.1186/s12864-018-5297-2

First genome-wide CNV mapping in FELIS CATUS using next generation sequencing data

F. Genova, M. Longeri, L. A. Lyons, A. Bagnato, Barbara Gandolfi, Danielle Aberdein, Paulo C. Alves, Gregory S. Barsh, Holly C. Beale, Tomas F. Bergström, Adam R. Boyko, Jeffrey A. Brockman, Marta G. Castelhano, Patricia P. Chan, Brian W. Davis, Ottmar Distl, Nicholas H. Dodman, N. Matthew Ellinwood, Jonathan E. Fogle, Oliver P. FormanDorian J. Garrick, Jens Häggström, Christopher R. Helps, Marjo K. Hytönen, Daniel M. Ibrahim, Maria Kaukonen, Christopher B. Kaelin, Emilie Leclerc, Teri L. Lear, Tosso Leeb, Hannes Lohi, Darío G. Lupiáñez, Mark A. Magnuson, Richard Malik, Michael J. Montague, John S. Munday, William J. Murphy, Elaine A. Ostrander, Niels C. Pedersen, Simon M. Petersen-Jones, Max F. Rothschild, Beth Shapiro, Joshua A. Stern, William F. Swanson, Karen A. Terio, Rory J. Todhunter, Yu Ueda, Wesley C. Warren, Elizabeth A. Wilcox, Julia H. Wildschutte, Edward I. Ginns, M. G. Strillacci

Research output: Contribution to journal › Article › peer-review

Abstract

Background: Copy Number Variations (CNVs) have becoming very significant variants, representing a major source of genomic variation. CNVs involvement in phenotypic expression and different diseases has been widely demonstrated in humans as well as in many domestic animals. However, genome wide investigation on these structural variations is still missing in Felis catus. The present work is the first CNV mapping from a large data set of Next Generation Sequencing (NGS) data in the domestic cat, performed within the 99 Lives Consortium. Results: Reads have been mapped on the reference assembly-6.2 by Maverix Biomics. CNV detection with cn.MOPS and CNVnator detected 592 CNVs. These CNVs were used to obtain 154 CNV Regions (CNVRs) with BedTools, including 62 singletons. CNVRs covered 0.26% of the total cat genome with 129 losses, 19 gains and 6 complexes. Cluster Analysis and Principal Component Analysis of the detected CNVRs showed that breeds tend to cluster together as well as cats sharing the same geographical origins. The 46 genes identified within the CNVRs were annotated. Conclusion: This study has improved the genomic characterization of 14 cat breeds and has provided CNVs information that can be used for studies of traits in cats. It can be considered a sound starting point for genomic CNVs identification in this species.

Original language	English (US)
Article number	895
Journal	BMC genomics
Volume	19
Issue number	1
DOIs	https://doi.org/10.1186/s12864-018-5297-2
State	Published - Dec 10 2018

Keywords

CNV
CNVR
CNVnator
Cat breeds
Cn.MOPS
Felis catus
NGS

ASJC Scopus subject areas

Biotechnology
Genetics

Online availability

10.1186/s12864-018-5297-2

Library availability

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Genova, F., Longeri, M., Lyons, L. A., Bagnato, A., Gandolfi, B., Aberdein, D., Alves, P. C., Barsh, G. S., Beale, H. C., Bergström, T. F., Boyko, A. R., Brockman, J. A., Castelhano, M. G., Chan, P. P., Davis, B. W., Distl, O., Dodman, N. H., Matthew Ellinwood, N., Fogle, J. E., ... Strillacci, M. G. (2018). First genome-wide CNV mapping in FELIS CATUS using next generation sequencing data. BMC genomics, 19(1), Article 895. https://doi.org/10.1186/s12864-018-5297-2

Genova, F, Longeri, M, Lyons, LA, Bagnato, A, Gandolfi, B, Aberdein, D, Alves, PC, Barsh, GS, Beale, HC, Bergström, TF, Boyko, AR, Brockman, JA, Castelhano, MG, Chan, PP, Davis, BW, Distl, O, Dodman, NH, Matthew Ellinwood, N, Fogle, JE, Forman, OP, Garrick, DJ, Häggström, J, Helps, CR, Hytönen, MK, Ibrahim, DM, Kaukonen, M, Kaelin, CB, Leclerc, E, Lear, TL, Leeb, T, Lohi, H, Lupiáñez, DG, Magnuson, MA, Malik, R, Montague, MJ, Munday, JS, Murphy, WJ, Ostrander, EA, Pedersen, NC, Petersen-Jones, SM, Rothschild, MF, Shapiro, B, Stern, JA, Swanson, WF, Terio, KA, Todhunter, RJ, Ueda, Y, Warren, WC, Wilcox, EA, Wildschutte, JH, Ginns, EI & Strillacci, MG 2018, 'First genome-wide CNV mapping in FELIS CATUS using next generation sequencing data', BMC genomics, vol. 19, no. 1, 895. https://doi.org/10.1186/s12864-018-5297-2

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title = "First genome-wide CNV mapping in FELIS CATUS using next generation sequencing data",

abstract = "Background: Copy Number Variations (CNVs) have becoming very significant variants, representing a major source of genomic variation. CNVs involvement in phenotypic expression and different diseases has been widely demonstrated in humans as well as in many domestic animals. However, genome wide investigation on these structural variations is still missing in Felis catus. The present work is the first CNV mapping from a large data set of Next Generation Sequencing (NGS) data in the domestic cat, performed within the 99 Lives Consortium. Results: Reads have been mapped on the reference assembly-6.2 by Maverix Biomics. CNV detection with cn.MOPS and CNVnator detected 592 CNVs. These CNVs were used to obtain 154 CNV Regions (CNVRs) with BedTools, including 62 singletons. CNVRs covered 0.26% of the total cat genome with 129 losses, 19 gains and 6 complexes. Cluster Analysis and Principal Component Analysis of the detected CNVRs showed that breeds tend to cluster together as well as cats sharing the same geographical origins. The 46 genes identified within the CNVRs were annotated. Conclusion: This study has improved the genomic characterization of 14 cat breeds and has provided CNVs information that can be used for studies of traits in cats. It can be considered a sound starting point for genomic CNVs identification in this species.",

keywords = "CNV, CNVR, CNVnator, Cat breeds, Cn.MOPS, Felis catus, NGS",

author = "F. Genova and M. Longeri and Lyons, {L. A.} and A. Bagnato and Barbara Gandolfi and Danielle Aberdein and Alves, {Paulo C.} and Barsh, {Gregory S.} and Beale, {Holly C.} and Bergstr{\"o}m, {Tomas F.} and Boyko, {Adam R.} and Brockman, {Jeffrey A.} and Castelhano, {Marta G.} and Chan, {Patricia P.} and Davis, {Brian W.} and Ottmar Distl and Dodman, {Nicholas H.} and {Matthew Ellinwood}, N. and Fogle, {Jonathan E.} and Forman, {Oliver P.} and Garrick, {Dorian J.} and Jens H{\"a}ggstr{\"o}m and Helps, {Christopher R.} and Hyt{\"o}nen, {Marjo K.} and Ibrahim, {Daniel M.} and Maria Kaukonen and Kaelin, {Christopher B.} and Emilie Leclerc and Lear, {Teri L.} and Tosso Leeb and Hannes Lohi and Lupi{\'a}{\~n}ez, {Dar{\'i}o G.} and Magnuson, {Mark A.} and Richard Malik and Montague, {Michael J.} and Munday, {John S.} and Murphy, {William J.} and Ostrander, {Elaine A.} and Pedersen, {Niels C.} and Petersen-Jones, {Simon M.} and Rothschild, {Max F.} and Beth Shapiro and Stern, {Joshua A.} and Swanson, {William F.} and Terio, {Karen A.} and Todhunter, {Rory J.} and Yu Ueda and Warren, {Wesley C.} and Wilcox, {Elizabeth A.} and Wildschutte, {Julia H.} and Ginns, {Edward I.} and Strillacci, {M. G.}",

note = "Publisher Copyright: {\textcopyright} 2018 The Author(s).",

year = "2018",

month = dec,

day = "10",

doi = "10.1186/s12864-018-5297-2",

language = "English (US)",

volume = "19",

journal = "BMC genomics",

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T1 - First genome-wide CNV mapping in FELIS CATUS using next generation sequencing data

AU - Genova, F.

AU - Longeri, M.

AU - Lyons, L. A.

AU - Bagnato, A.

AU - Gandolfi, Barbara

AU - Aberdein, Danielle

AU - Alves, Paulo C.

AU - Barsh, Gregory S.

AU - Beale, Holly C.

AU - Bergström, Tomas F.

AU - Boyko, Adam R.

AU - Brockman, Jeffrey A.

AU - Castelhano, Marta G.

AU - Chan, Patricia P.

AU - Davis, Brian W.

AU - Distl, Ottmar

AU - Dodman, Nicholas H.

AU - Matthew Ellinwood, N.

AU - Fogle, Jonathan E.

AU - Forman, Oliver P.

AU - Garrick, Dorian J.

AU - Häggström, Jens

AU - Helps, Christopher R.

AU - Hytönen, Marjo K.

AU - Ibrahim, Daniel M.

AU - Kaukonen, Maria

AU - Kaelin, Christopher B.

AU - Leclerc, Emilie

AU - Lear, Teri L.

AU - Leeb, Tosso

AU - Lohi, Hannes

AU - Lupiáñez, Darío G.

AU - Magnuson, Mark A.

AU - Malik, Richard

AU - Montague, Michael J.

AU - Munday, John S.

AU - Murphy, William J.

AU - Ostrander, Elaine A.

AU - Pedersen, Niels C.

AU - Petersen-Jones, Simon M.

AU - Rothschild, Max F.

AU - Shapiro, Beth

AU - Stern, Joshua A.

AU - Swanson, William F.

AU - Terio, Karen A.

AU - Todhunter, Rory J.

AU - Ueda, Yu

AU - Warren, Wesley C.

AU - Wilcox, Elizabeth A.

AU - Wildschutte, Julia H.

AU - Ginns, Edward I.

AU - Strillacci, M. G.

PY - 2018/12/10

Y1 - 2018/12/10

N2 - Background: Copy Number Variations (CNVs) have becoming very significant variants, representing a major source of genomic variation. CNVs involvement in phenotypic expression and different diseases has been widely demonstrated in humans as well as in many domestic animals. However, genome wide investigation on these structural variations is still missing in Felis catus. The present work is the first CNV mapping from a large data set of Next Generation Sequencing (NGS) data in the domestic cat, performed within the 99 Lives Consortium. Results: Reads have been mapped on the reference assembly-6.2 by Maverix Biomics. CNV detection with cn.MOPS and CNVnator detected 592 CNVs. These CNVs were used to obtain 154 CNV Regions (CNVRs) with BedTools, including 62 singletons. CNVRs covered 0.26% of the total cat genome with 129 losses, 19 gains and 6 complexes. Cluster Analysis and Principal Component Analysis of the detected CNVRs showed that breeds tend to cluster together as well as cats sharing the same geographical origins. The 46 genes identified within the CNVRs were annotated. Conclusion: This study has improved the genomic characterization of 14 cat breeds and has provided CNVs information that can be used for studies of traits in cats. It can be considered a sound starting point for genomic CNVs identification in this species.

AB - Background: Copy Number Variations (CNVs) have becoming very significant variants, representing a major source of genomic variation. CNVs involvement in phenotypic expression and different diseases has been widely demonstrated in humans as well as in many domestic animals. However, genome wide investigation on these structural variations is still missing in Felis catus. The present work is the first CNV mapping from a large data set of Next Generation Sequencing (NGS) data in the domestic cat, performed within the 99 Lives Consortium. Results: Reads have been mapped on the reference assembly-6.2 by Maverix Biomics. CNV detection with cn.MOPS and CNVnator detected 592 CNVs. These CNVs were used to obtain 154 CNV Regions (CNVRs) with BedTools, including 62 singletons. CNVRs covered 0.26% of the total cat genome with 129 losses, 19 gains and 6 complexes. Cluster Analysis and Principal Component Analysis of the detected CNVRs showed that breeds tend to cluster together as well as cats sharing the same geographical origins. The 46 genes identified within the CNVRs were annotated. Conclusion: This study has improved the genomic characterization of 14 cat breeds and has provided CNVs information that can be used for studies of traits in cats. It can be considered a sound starting point for genomic CNVs identification in this species.

KW - CNV

KW - CNVR

KW - CNVnator

KW - Cat breeds

KW - Cn.MOPS

KW - Felis catus

KW - NGS

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U2 - 10.1186/s12864-018-5297-2

DO - 10.1186/s12864-018-5297-2

M3 - Article

C2 - 30526495

AN - SCOPUS:85058212250

SN - 1471-2164

VL - 19

JO - BMC genomics

JF - BMC genomics

IS - 1

M1 - 895

ER -

First genome-wide CNV mapping in FELIS CATUS using next generation sequencing data

Abstract

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