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Clinical utility of the low-density Infinium QC genotyping Array in a genomics-based diagnostics laboratory

Overview of attention for article published in BMC Medical Genomics, October 2017
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Title
Clinical utility of the low-density Infinium QC genotyping Array in a genomics-based diagnostics laboratory
Published in
BMC Medical Genomics, October 2017
DOI 10.1186/s12920-017-0297-7
Pubmed ID
Authors

Petr Ponomarenko, Alex Ryutov, Dennis T. Maglinte, Ancha Baranova, Tatiana V. Tatarinova, Xiaowu Gai

Abstract

With 15,949 markers, the low-density Infinium QC Array-24 BeadChip enables linkage analysis, HLA haplotyping, fingerprinting, ethnicity determination, mitochondrial genome variations, blood groups and pharmacogenomics. It represents an attractive independent QC option for NGS-based diagnostic laboratories, and provides cost-efficient means for determining gender, ethnic ancestry, and sample kinships, that are important for data interpretation of NGS-based genetic tests. We evaluated accuracy and reproducibility of Infinium QC genotyping calls by comparing them with genotyping data of the same samples from other genotyping platforms, whole genome/exome sequencing. Accuracy and robustness of determining gender, provenance, and kinships were assessed. Concordance of genotype calls between Infinium QC and other platforms was above 99%. Here we show that the chip's ancestry informative markers are sufficient for ethnicity determination at continental and sometimes subcontinental levels, with assignment accuracy varying with the coverage for a particular region and ethnic groups. Mean accuracies of provenance prediction at a regional level were varied from 81% for Asia, to 89% for Americas, 86% for Africa, 97% for Oceania, 98% for Europe, and 100% for India. Mean accuracy of ethnicity assignment predictions was 63%. Pairwise concordances of AFR samples with the samples from any other super populations were the lowest (0.39-0.43), while the concordances within the same population were relatively high (0.55-0.61). For all populations except African, cross-population comparisons were similar in their concordance ranges to the range of within-population concordances (0.54-0.57). Gender determination was correct in all tested cases. Our results indicate that the Infinium QC Array-24 chip is suitable for cost-efficient, independent QC assaying in the settings of an NGS-based molecular diagnostic laboratory; hence, we recommend its integration into the standard laboratory workflow. Low-density chips can provide sample-specific measures for variant call accuracy, prevent sample mix-ups, validate self-reported ethnicities, and detect consanguineous cases. Integration of low-density chips into QC procedures aids proper interpretation of candidate sequence variants. To enhance utility of this low-density chip, we recommend expansion of ADME and mitochondrial markers. Inexpensive Infinium-like low-density human chips have a potential to become a "Swiss army knife" among genotyping assays suitable for many applications requiring high-throughput assays.

Twitter Demographics

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Mendeley readers

The data shown below were compiled from readership statistics for 31 Mendeley readers of this research output. Click here to see the associated Mendeley record.

Geographical breakdown

Country Count As %
Unknown 31 100%

Demographic breakdown

Readers by professional status Count As %
Student > Bachelor 5 16%
Student > Ph. D. Student 4 13%
Researcher 4 13%
Student > Master 4 13%
Other 3 10%
Other 3 10%
Unknown 8 26%
Readers by discipline Count As %
Medicine and Dentistry 6 19%
Biochemistry, Genetics and Molecular Biology 4 13%
Engineering 3 10%
Pharmacology, Toxicology and Pharmaceutical Science 2 6%
Agricultural and Biological Sciences 2 6%
Other 4 13%
Unknown 10 32%

Attention Score in Context

This research output has an Altmetric Attention Score of 1. This is our high-level measure of the quality and quantity of online attention that it has received. This Attention Score, as well as the ranking and number of research outputs shown below, was calculated when the research output was last mentioned on 09 October 2017.
All research outputs
#18,573,839
of 23,005,189 outputs
Outputs from BMC Medical Genomics
#867
of 1,230 outputs
Outputs of similar age
#247,660
of 323,390 outputs
Outputs of similar age from BMC Medical Genomics
#10
of 11 outputs
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We're also able to compare this research output to 11 others from the same source and published within six weeks on either side of this one. This one is in the 1st percentile – i.e., 1% of its contemporaries scored the same or lower than it.