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Research article
Yu Jiang
Northwest Agriculture and Forestry University
Corresponding Author
ORCiD: https://orcid.org/0000-0003-4821-3585
License:
This work is licensed under a CC BY 4.0 License. Read Full License
Background The non-reference sequences (NRS) represent structure variations in human genome with potential functional significance. However, besides the known insertions, it is currently unknown whether other types of structure variations with NRS exist. Results Here, we compared 31 human de novo assemblies with the current reference genome to identify the NRS and their location. We resolved the precise location of 6,113 NRS adding up to 12.8 Mb. Besides 1,571 insertions, we detected 3,041 alternate alleles, which were defined as having less than 90% (or none) identity with the reference alleles. These alternate alleles overlapped with 1,143 protein-coding genes including a putative novel MHC haplotype. Further, we demonstrated that the alternate alleles and their flanking regions had high content of tandem repeats, indicating that their origin was associated with tandem repeats. Conclusions Our study detected a large number of NRS including many alternate alleles which are previously uncharacterized. We suggested that the origin of alternate alleles was associated with tandem repeats. Our results enriched the spectrum of genetic variations in human genome.
Keywords
pan-genome, human genome, genomic variation, alternate alleles
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Peer Review Timeline
CURRENT STATUS: Published
View the published article at BMC Genomics.
Version 3
Posted 30 Sep, 2019
No community comments so far
Submission checks complete
On 06 Nov, 2019
Editorial decision: Accept
On 17 Sep, 2019
No comments provided
Editorial decision: Minor revision
On 10 Sep, 2019
Editor assigned
On 29 Aug, 2019
Submission checks complete
On 28 Aug, 2019
Editor invited
On 28 Aug, 2019
No comments provided
Review #2 received
Received 02 Aug, 2019
Editorial decision: Major revision
On 02 Aug, 2019
Review #1 received
Received 30 Jul, 2019
Reviewer #2 agreed
On 19 Jul, 2019
Reviewers invited
Invitations sent on 18 Jul, 2019
Reviewer #1 agreed
On 18 Jul, 2019
Submission checks complete
On 17 Jul, 2019
Editor assigned
On 04 Jul, 2019
Editor invited
On 03 Jul, 2019
First submitted
On 02 Jul, 2019
Metrics
Comments: 0
PDF Downloads: ...
HTML Views: ...
Subject Areas
Epigenetics & Genomics
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A new preprint design is coming!
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See the published version of this preprint at BMC Genomics.
This is a preprint, a preliminary version of a manuscript that has not completed peer review at a journal. Research Square does not conduct peer review prior to posting preprints. The posting of a preprint on this server should not be interpreted as an endorsement of its validity or suitability for dissemination as established information or for guiding clinical practice.
Learn more about In Review
Research article
Yu Jiang
Northwest Agriculture and Forestry University
Corresponding Author
ORCiD: https://orcid.org/0000-0003-4821-3585
Badges
Prescreen
This manuscript passed our Prescreen assessment
Complete author information
Appropriate declaration statements
Potential risks to human health
Prescreen
Peer Review Timeline
CURRENT STATUS: Published
View the published article at BMC Genomics.
Version 3
Posted 30 Sep, 2019
No community comments so far
Submission checks complete
On 06 Nov, 2019
Editorial decision: Accept
On 17 Sep, 2019
No comments provided
Editorial decision: Minor revision
On 10 Sep, 2019
Editor assigned
On 29 Aug, 2019
Submission checks complete
On 28 Aug, 2019
Editor invited
On 28 Aug, 2019
No comments provided
Review #2 received
Received 02 Aug, 2019
Editorial decision: Major revision
On 02 Aug, 2019
Review #1 received
Received 30 Jul, 2019
Reviewer #2 agreed
On 19 Jul, 2019
Reviewers invited
Invitations sent on 18 Jul, 2019
Reviewer #1 agreed
On 18 Jul, 2019
Submission checks complete
On 17 Jul, 2019
Editor assigned
On 04 Jul, 2019
Editor invited
On 03 Jul, 2019
First submitted
On 02 Jul, 2019
Metrics
Comments: 0
PDF Downloads: ...
HTML Views: ...
Subject Areas
Epigenetics & Genomics
License:
This work is licensed under a CC BY 4.0 License. Read Full License
View the published article at BMC Genomics.
Background The non-reference sequences (NRS) represent structure variations in human genome with potential functional significance. However, besides the known insertions, it is currently unknown whether other types of structure variations with NRS exist. Results Here, we compared 31 human de novo assemblies with the current reference genome to identify the NRS and their location. We resolved the precise location of 6,113 NRS adding up to 12.8 Mb. Besides 1,571 insertions, we detected 3,041 alternate alleles, which were defined as having less than 90% (or none) identity with the reference alleles. These alternate alleles overlapped with 1,143 protein-coding genes including a putative novel MHC haplotype. Further, we demonstrated that the alternate alleles and their flanking regions had high content of tandem repeats, indicating that their origin was associated with tandem repeats. Conclusions Our study detected a large number of NRS including many alternate alleles which are previously uncharacterized. We suggested that the origin of alternate alleles was associated with tandem repeats. Our results enriched the spectrum of genetic variations in human genome.
Figure 1
Figure 2
Figure 3
Figure 4
Figure 5
Figure 6
This is a list of supplementary files associated with this preprint. Click to download.
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