Evidence map›Paper›PMID 30764755›Full record

ArticleBMC genetics2019

Characterization of the extra copy of TPOX locus with tri-allelic pattern.

Qinrui Yang, Baonian Liu, Chengchen Shao, Yuxiang Zhou, Yining Yao, Yuyin Pan, Kuan Sun, Hongmei Xu, Chengtao Li, Ting Wei and 3 more

Abstract read
PubMed Full text at PMC Publisher
In one paragraph

Article in BMC genetics, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 6 papers.

0numbers the graph read from it
0cells of the map it votes in
6citing papers in PubMed
–field-weighted citation impact
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

6 citing papers in PubMed.

  1. Article
  2. Article
  3. Article
  4. Review
  5. Genetic analysis of tri-allelic patterns at the CODIS STR loci.Molecular genetics and genomics : MGG · 2020
    Article
  6. Article
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

13 authors.

Qinrui YangDepartment of Forensic Medicine, Shanghai Medical College of Fudan University, Shanghai, 200032, China.
Baonian LiuDepartment of Forensic Medicine, Shanghai Medical College of Fudan University, Shanghai, 200032, China.
Chengchen ShaoDepartment of Forensic Medicine, Shanghai Medical College of Fudan University, Shanghai, 200032, China.
Yuxiang ZhouDepartment of Forensic Medicine, Shanghai Medical College of Fudan University, Shanghai, 200032, China.
Yining YaoDepartment of Forensic Medicine, Shanghai Medical College of Fudan University, Shanghai, 200032, China.
Yuyin PanDepartment of Forensic Medicine, Shanghai Medical College of Fudan University, Shanghai, 200032, China.
Kuan SunDepartment of Forensic Medicine, Shanghai Medical College of Fudan University, Shanghai, 200032, China.
Hongmei XuDepartment of Forensic Medicine, Shanghai Medical College of Fudan University, Shanghai, 200032, China.
Chengtao LiShanghai Key Laboratory of Forensic Medicine, Institute of Forensic Science, Ministry of Justice, Shanghai, 200063, China.
Ting WeiNovogene Co., LTD, Beijing, 100142, People's Republic of China.
Yueqin ZhouDepartment of Forensic Medicine, Shanghai Medical College of Fudan University, Shanghai, 200032, China.
Qiqun TangDepartment of Biochemistry and Molecular Biology, Shanghai Medical College of Fudan University, Shanghai, 200032, China.
Jianhui XieDepartment of Forensic Medicine, Shanghai Medical College of Fudan University, Shanghai, 200032, China. jhxie@fudan.edu.cn.ORCID 0000-0003-4989-0588

Funding

No grant is acknowledged in the PubMed record.

6 · The paper itself

Abstract

backgroundAn STR locus with tri-allelic pattern is occasionally observed in routine forensic casework. The extra copy of TPOX locus with tri-allelic pattern in populations has been assumed to be inserted into an X chromosome, which took place forth before the Bantu expansion in Africa. Nonetheless, the exact location of the duplication and the form of rearrangement in the human genome has not been clarified yet.

resultsIn this study, we investigated the extra copy of type 2 tri-allelic pattern at TPOX in various populations. While allele 10 is the major third allele in Africa, allele 11 appears more frequent in America and overwhelming in Chinese and Korean populations, which might attribute to the population substructures. Results from the investigation of family cases showed that the transmission of the extra allele had a similar genetic pattern of autosomal genes. Furthermore, a whole-genome sequencing followed by bioinformatics analysis revealed that the intact form of chromosomal duplication and rearrangement occurred ~ 407 kb away from the authentic TPOX locus on chromosome 2 in two cases. The breakpoints of the insertion were further validated in most other tri-allelic subjects, which can imply the identical origin from the ancestral extra copy. Nevertheless, de novo chromosomal duplication and rearrangement at thyroid peroxidase gene occur in populations.

conclusionsInstead of the extra allele 10 in African populations, the main third allele at TPOX with tri-allelic pattern is allele 11 in Chinese and Korean populations. The insertion of the extra copy into chromosome 2 occurs in most subjects with tri-allelic pattern at TPOX and demonstrates the transmission of the third allele from parents to offspring. The breakpoints of the ancestral extra copy are defined, which shows evidence of its inheritance from African populations. In addition, the simple validation method would help improve tri-allelic pattern calling, distinguish de novo chromosomal rearrangements, and also count the frequencies among different geographic regions. Therefore, the statistical interpretation of tri-allelic pattern at TPOX could be enhanced during forensic practice.

Indexed as

AllelesGene DosageGene RearrangementGenetic LociGenotyping TechniquesHumansChromosome 2RecombinationShort tandem repeatsTPOXTri-allelic pattern

Identifiers

PMID30764755
PMCPMC6376737

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.