Dataset Information

Validation of whole genome sequencing from dried blood spots.

ABSTRACT:

Background

Dried blood spots (DBS) are a relatively inexpensive source of nucleic acids and are easy to collect, transport, and store in large-scale field surveys, especially in resource-limited settings. However, their performance in whole-genome sequencing (WGS) relative to that of venous blood DNA has not been analyzed for various downstream applications.

Methods

This study compares the WGS performance of DBS paired with venous blood samples collected from 12 subjects.

Results

Results of standard quality checks of coverage, base quality, and mapping quality were found to be near identical between DBS and venous blood. Concordance for single-nucleotide variants, insertions and deletions, and copy number variants was high between these two sample types. Additionally, downstream analyses typical of population-based studies were performed, such as mitochondrial heteroplasmy detection, haplotype analysis, mitochondrial copy number changes, and determination of telomere lengths. The absolute mitochondrial copy number values were higher for DBS than for venous blood, though the trend in sample-to-sample variation was similar between DBS and blood. Telomere length estimates in most DBS samples were on par with those from venous blood.

Conclusion

DBS samples can serve as a robust and feasible alternative to venous blood for studies requiring WGS analysis.

SUBMITTER: Agrawal P

PROVIDER: S-EPMC8056537 | biostudies-literature | 2021 Apr

REPOSITORIES: biostudies-literature

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Publications

Validation of whole genome sequencing from dried blood spots.

Agrawal Pooja P Katragadda Shanmukh S Hariharan Arun K AK Raghavendrachar Vijayashree Gauribidanur VG Agarwal Arunika A Dayalu Rashmi R Awasthy Disha D Sharma Sanjay C SC Sivasamy Yasodha Kannan YK Lakshmana P P Shanmugam Ashwini A Veeramachaneni Vamsi V Gupta Vaijayanti V Vani B P BP Subaiya Lekha L Syamala T S TS Hariharan Ramesh R Chandru Vijay V Bloom David E DE

BMC medical genomics 20210420 1

<h4>Background</h4>Dried blood spots (DBS) are a relatively inexpensive source of nucleic acids and are easy to collect, transport, and store in large-scale field surveys, especially in resource-limited settings. However, their performance in whole-genome sequencing (WGS) relative to that of venous blood DNA has not been analyzed for various downstream applications.<h4>Methods</h4>This study compares the WGS performance of DBS paired with venous blood samples collected from 12 subjects.<h4>Resul ...[more]

PMID: 33879142

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Project description:IntroductionHeel pricks are performed on newborns for diagnostic screenings of various pre-symptomatic metabolic and genetic diseases. Excess blood is spotted on Guthrie cards and archived by many states in biobanks for follow-up diagnoses and public health research. However, storage environment may vary across biobanks and across time within biobanks. With increased applications of DNA extracted from spots for genetic studies, identifying factors associated with genotyping success is critical to maximize DNA quality for future studies.MethodWe evaluated 399 blood spots, which were part of a genome-wide association study of childhood leukemia risk in children with Down syndrome, archived at the Michigan Neonatal Biobank between 1992 and 2008. High quality DNA was defined as having post-quality control call rate ≥ 99.0% based on the Illumina GenomeStudio 2.0 GenCall algorithm after processing the samples on the Illumina Infinium Global Screening Array. Bivariate analyses and multivariable logistic regression models were applied to evaluate effects of storage environment and storage duration on DNA genotyping quality.ResultsBoth storage environment and duration were associated with sample genotyping call rates (p-values < 0.001). Sample call rates were associated with storage duration independent of storage environment (p-trend = 0.006 for DBS archived in an uncontrolled environment and p-trend = 0.002 in a controlled environment). However, 95% of the total sample had high genotyping quality with a call rate ≥ 95.0%, a standard threshold for acceptable sample quality in many genetic studies.ConclusionBlood spot DNA quality was lower in samples archived in uncontrolled storage environments and for samples archived for longer durations. Still, regardless of storage environment or duration, neonatal biobanks including the Michigan Neonatal Biobanks can provide access to large collections of spots with DNA quality acceptable for most genotyping studies.

Dataset Information

Validation of whole genome sequencing from dried blood spots.

Background

Methods

Results

Conclusion

Publications

Validation of whole genome sequencing from dried blood spots.

Similar Datasets

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