Evidence map›Paper›PMID 33051442›Full record

ArticleScientific data2020

Whole genome sequencing data of multiple individuals of Pakistani descent.

Shahid Y Khan, Muhammad Ali, Mei-Chong W Lee, Zhiwei Ma, Pooja Biswas, Asma A Khan, Muhammad Asif Naeem, Saima Riazuddin, Sheikh Riazuddin, Radha Ayyagari and 2 more

Abstract readDataset
PubMed Full text at PMC Publisher
In one paragraph

Article in Scientific data, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 2 papers.

0numbers the graph read from it
0cells of the map it votes in
2citing 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

2 citing papers in PubMed.

  1. Review
  2. 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

12 authors.

Shahid Y KhanThe Wilmer Eye Institute, Johns Hopkins University School of Medicine, Baltimore, MD, 21287, USA.
Muhammad AliThe Wilmer Eye Institute, Johns Hopkins University School of Medicine, Baltimore, MD, 21287, USA.
Mei-Chong W LeeDepartment of Computer Science, San José State University, San José, CA, 95192, USA.
Zhiwei MaOphthalmic Genetics and Visual Function Branch, National Eye Institute, National Institutes of Health, Bethesda, MD, 20892, USA.
Pooja BiswasShiley Eye Institute, University of California San Diego, La Jolla, CA, 92093, USA.
Asma A KhanNational Centre of Excellence in Molecular Biology, University of the Punjab, Lahore, 53700, Pakistan.
Muhammad Asif NaeemNational Centre of Excellence in Molecular Biology, University of the Punjab, Lahore, 53700, Pakistan.
Saima RiazuddinDepartment of Otorhinolaryngology-Head & Neck Surgery, University of Maryland School Medicine, Baltimore, MD, 21201, USA.ORCID 0000-0002-8645-4761
Sheikh RiazuddinNational Centre of Excellence in Molecular Biology, University of the Punjab, Lahore, 53700, Pakistan.
Radha AyyagariShiley Eye Institute, University of California San Diego, La Jolla, CA, 92093, USA.
J Fielding HejtmancikOphthalmic Genetics and Visual Function Branch, National Eye Institute, National Institutes of Health, Bethesda, MD, 20892, USA.ORCID 0000-0002-4788-0362
S Amer RiazuddinThe Wilmer Eye Institute, Johns Hopkins University School of Medicine, Baltimore, MD, 21287, USA. riazuddin@jhmi.edu.

Funding

Genetics and Functional Studies of Autosomal Recessive Neurological DisordersR01NS107428 · NINDS · UNIVERSITY OF MARYLAND BALTIMORE · PI Saima Riazuddin · 2018 to 2026
$4.7M
Identification of Lens Function Through Analysis of Human CataractsR01EY022714 · NEI · JOHNS HOPKINS UNIVERSITY · PI RIAZUDDIN, AMER · 2014 to 2018
$2.0M
NEI NIH HHS R01 EY022714NINDS NIH HHS R01 NS107428
6 · The paper itself

Abstract

Here we report whole genome sequencing of four individuals (H3, H4, H5, and H6) from a family of Pakistani descent. Whole genome sequencing yielded 1084.92, 894.73, 1068.62, and 1005.77 million mapped reads corresponding to 162.73, 134.21, 160.29, and 150.86 Gb sequence data and 52.49x, 43.29x, 51.70x, and 48.66x average coverage for H3, H4, H5, and H6, respectively. We identified 3,529,659, 3,478,495, 3,407,895, and 3,426,862 variants in the genomes of H3, H4, H5, and H6, respectively, including 1,668,024 variants common in the four genomes. Further, we identified 42,422, 39,824, 28,599, and 35,206 novel variants in the genomes of H3, H4, H5, and H6, respectively. A major fraction of the variants identified in the four genomes reside within the intergenic regions of the genome. Single nucleotide polymorphism (SNP) genotype based comparative analysis with ethnic populations of 1000 Genomes database linked the ancestry of all four genomes with the South Asian populations, which was further supported by mitochondria based haplogroup analysis. In conclusion, we report whole genome sequencing of four individuals of Pakistani descent.

Indexed as

Genome, HumanWhole Genome SequencingHumansPakistanPolymorphism, Single Nucleotide

Identifiers

PMID33051442
PMCPMC7555865

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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.