Evidence map›Paper›PMID 35300589›Full record

ArticleBMC genomics2022

Towards the detection of copy number variation from single sperm sequencing in cattle.

Liu Yang, Yahui Gao, Adam Oswalt, Lingzhao Fang, Clarissa Boschiero, Mahesh Neupane, Charles G Sattler, Cong-Jun Li, Eyal Seroussi, Lingyang Xu and 8 more

Open access · goldAbstract read
PubMed Full text at PMC Publisher
In one paragraph

Article in BMC genomics, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 3 papers.

0numbers the graph read from it
0cells of the map it votes in
3citing papers in PubMed
0.4field-weighted citation impact, top 34% of its field
1 · What the graph read from it

What it found

Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.

The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.

2 · The registry

The trial behind it

Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.

Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.

3 · Its place in the literature

Who cites it

3 citing papers in PubMed, 2 citations in OpenAlex.

  1. Article
  2. Article
  3. Harnessing male germline epigenomics for the genetic improvement in cattle.Journal of animal science and biotechnology · 2023
    Review
4 · The record

Corrections and comments

PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.

5 · Who and what money

Authors and funding

18 authors at 8 institutions in 4 countries.

Liu Yang *Animal Genomics and Improvement Laboratory, Henry A. Wallace Beltsville Agricultural Research Center, Agricultural Research Service, USDA, Beltsville, MD, 20705, USA.
Yahui Gao *Animal Genomics and Improvement Laboratory, Henry A. Wallace Beltsville Agricultural Research Center, Agricultural Research Service, USDA, Beltsville, MD, 20705, USA.
Adam OswaltSelect Sires Inc, 11740 U.S. 42 North, Plain City, OH, 43064, USA.
Lingzhao FangMRC Human Genetics Unit at the Institute of Genetics and Cancer, The University of Edinburgh, Edinburgh, EH4 2XU, UK.
Clarissa BoschieroAnimal Genomics and Improvement Laboratory, Henry A. Wallace Beltsville Agricultural Research Center, Agricultural Research Service, USDA, Beltsville, MD, 20705, USA.
Mahesh NeupaneAnimal Genomics and Improvement Laboratory, Henry A. Wallace Beltsville Agricultural Research Center, Agricultural Research Service, USDA, Beltsville, MD, 20705, USA.
Charles G SattlerSelect Sires Inc, 11740 U.S. 42 North, Plain City, OH, 43064, USA.
Cong-Jun LiAnimal Genomics and Improvement Laboratory, Henry A. Wallace Beltsville Agricultural Research Center, Agricultural Research Service, USDA, Beltsville, MD, 20705, USA.
Eyal SeroussiAgricultural Research Organization (ARO), Institute of Animal Science, HaMaccabim Road, P.O.B 15159, 7528809, Volcani CenterRishon LeTsiyon, Israel.
Lingyang XuInnovation Team of Cattle Genetic Breeding, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100193, China.
Lv YangKey Laboratory of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education & College of Animal Science and Technology, Huazhong Agricultural University, Wuhan, 430070, China.
Li LiCollege of Animal Science and Technology, Sichuan Agricultural University, Chengdu, 611130, China.
Hongping ZhangCollege of Animal Science and Technology, Sichuan Agricultural University, Chengdu, 611130, China.
Benjamin D RosenAnimal Genomics and Improvement Laboratory, Henry A. Wallace Beltsville Agricultural Research Center, Agricultural Research Service, USDA, Beltsville, MD, 20705, USA.
Curtis P Van TassellAnimal Genomics and Improvement Laboratory, Henry A. Wallace Beltsville Agricultural Research Center, Agricultural Research Service, USDA, Beltsville, MD, 20705, USA.
Yang ZhouKey Laboratory of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education & College of Animal Science and Technology, Huazhong Agricultural University, Wuhan, 430070, China.
Li MaDepartment of Animal and Avian Sciences, University of Maryland, College Park, MD, 20742, USA. lima@umd.edu.
George E LiuAnimal Genomics and Improvement Laboratory, Henry A. Wallace Beltsville Agricultural Research Center, Agricultural Research Service, USDA, Beltsville, MD, 20705, USA. George.Liu@ars.usda.gov.
Beltsville Agricultural Research Center · USAgricultural Research Service · USHuazhong Agricultural University · CNSichuan Agricultural University · CNUniversity of Maryland, College Park · USAgricultural Research Organization · ILInstitute of Animal Sciences · CNUniversity of Edinburgh · GB

Funding

National Institute of Food and Agriculture 2016-67015-24886National Institute of Food and Agriculture 2019-67015-29321United States - Israel Binational Agricultural Research and Development Fund US-4997-17
6 · The paper itself

Abstract

backgroundCopy number variation (CNV) has been routinely studied using bulk-cell sequencing. However, CNV is not well studied on the single-cell level except for humans and a few model organisms.

resultsWe sequenced 143 single sperms of two Holstein bulls, from which we predicted CNV events using 14 single sperms with deep sequencing. We then compared the CNV results derived from single sperms with the bulk-cell sequencing of one bull's family trio of diploid genomes. As a known CNV hotspot, segmental duplications were also predicted using the bovine ARS-UCD1.2 genome. Although the trio CNVs validated only some single sperm CNVs, they still showed a distal chromosomal distribution pattern and significant associations with segmental duplications and satellite repeats.

conclusionOur preliminary results pointed out future research directions and highlighted the importance of uniform whole genome amplification, deep sequence coverage, and dedicated software pipelines for CNV detection using single cell sequencing data.

Indexed as

DNA Copy Number VariationsGenomeAnimalsCattleMaleSegmental Duplications, GenomicSequence Analysis, DNASpermatozoaCattleCopy number variationSingle sperm sequencing

Identifiers

PMID35300589
PMCPMC8928590
OpenAlexW4220933960

What OpenQuestion holds

Textmetadata
LicenceCC BY
Read underepoch 390

Registered trials

None linked

Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.