The future of DNA sequencing

Green, Eric D.; Rubin, Edward M.; Olson, Maynard V.

doi:10.1038/550179a

Cited by 57 publications

(39 citation statements)

References 9 publications

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“…To date, approximately 4-6 million pregnants have got fetal cfDNA screening (Green, Rubin, & Olson, 2017). And, recent studies reveal there is 40%-70% decrease in invasive prenatal procedures since 2012 (Hui, Hutchinson, Poulton, & Halliday, 2017;Warsof, Larion, & Abuhamad, 2015).…”

Section: Introductionmentioning

confidence: 99%

Targeted fetal cell‐free DNA screening for aneuploidies in 4,594 pregnancies: Single center study

Koç

Kaya

Özyılmaz

et al. 2019

Molec Gen & Gen Med

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Background Next‐generation sequencing (NGS) and discovery of fetal cell‐free DNA (cfDNA) in the maternal circulation render possible prenatal screening for trisomy 21 (Down syndrome), trisomy 18, trisomy 13, and sex chromosome aneuploidies. The approach is called “fetal cfDNA screening” and in contrast to noninvasive conventional serum screening, it provides the identification of 98%–99% of fetuses with Down syndrome. Methods Retrospective analysis of targeted noninvasive prenatal testing (NIPT) (Clarigo Test) pregnancies with moderate risk, which we have reported between 2016 and 2018 years is presented. Two separate laboratory workflows and NGS platforms are used for the same targeted NIPT analysis. Results In total, 4,594 pregnant women were investigated. Initial 3,594 cases are studied by MiSeq platform, the last 1,000 cases by NextSeq. Failure rate for MiSeq platform is 10.9% and for NextSeq is 8.7%. Automatically reported cases constitute 75% of the MiSeq group and 87% of the NextSeq group. Conclusions Targeted NIPT results suggest that MiSeq platform could be used for NIPT which would be an essential option particularly for laboratories with low sample flow. And, the NextSeq platform has easier wet lab process and also increased success rate in automatic reporting which is suitable for centers with high number of NIPT cases.

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Section: Introductionmentioning

confidence: 99%

Targeted fetal cell‐free DNA screening for aneuploidies in 4,594 pregnancies: Single center study

Koç

Kaya

Özyılmaz

et al. 2019

Molec Gen & Gen Med

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“…Since its incorporation into clinical care in the United States in October 2011, massively parallel sequencing of circulating cell‐free (cf) DNA in maternal plasma—noninvasive prenatal testing—has revolutionized prenatal screening and diagnosis for fetal aneuploidy. It is the largest and fastest growing assay in genomic medicine, and up to 6 million tests have been performed globally to date . Compared with serum screening, cfDNA has better sensitivities, specificities, positive and negative predictive values, and significantly lower false‐positive rates .…”

Section: Introductionmentioning

confidence: 99%

“…It is the largest and fastest growing assay in genomic medicine, and up to 6 million tests have been performed globally to date. 1 Compared with serum screening, cfDNA has better sensitivities, specificities, positive and negative predictive values, and significantly lower false-positive rates. [2][3][4][5][6][7][8][9][10][11][12][13][14][15] Multiple professional societies, such as the American College of Obstetricians and Gynecologists, the Society for Maternal Fetal Medicine, the International Society for Prenatal Diagnosis, and the American College of Medical Genetics and Genomics, have endorsed offering cfDNA after pretest counseling to women at high risk for having a fetus with a chromosome aneuploidy.…”

Section: Introductionmentioning

confidence: 99%

Biological explanations for discordant noninvasive prenatal test results: Preliminary data and lessons learned

et al. 2018

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“…2 Variant calling was finally performed from this filtered data set, while given the number of included samples, only alleles with detected minor allele frequencies (MAF) above 5% were considered for further statistical and experimental analyses. However, we anticipate that increasing the number of aggregated samples would allow to safely decrease this threshold even to rare variants which seems to be feasible especially when considering the readily increasing worldwide popularity of NIPT testing (Green et al 2017;Shendure et al 2017).…”

Section: Discussionmentioning

confidence: 99%

Non-invasive prenatal testing as a valuable source of population specific allelic frequencies

Budiš

Gazdarica

Radvánszky

et al. 2018

Preprint

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Low-coverage massively parallel genome sequencing for non-invasive prenatal testing (NIPT) of common aneuploidies is one of the most rapidly adopted and relatively low-cost DNA tests. Since aggregation of reads from a large number of samples allows overcoming the problems of extremely low coverage of individual samples, we describe the possible re-use of the data generated during NIPT testing for genome scale population specific frequency determination of small DNA variants, requiring no additional costs except of those for the NIPT test itself. We applied our method to a data set comprising of 1,548 original NIPT test results and evaluated the findings on different levels, from in silico population frequency comparisons up to wet lab validation analyses using a gold-standard method. The revealed high reliability of variant calling and allelic frequency determinations suggest that these NIPT data could serve as valuable alternatives to large scale population studies even for smaller countries around the world. Langmead B, Salzberg SL. 2012. Fast gapped-read alignment with Bowtie 2. Nature methods frequencies of variants in our sample set and six different ExAC populations. Results are shown separately for (a) SNVs based on 68,326 variants; and (b) indels based on 2,909. In both cases, only those variants were used, which were simultaneously identified in each data subset with MAF higher than 5%. AFR = African/African American, AMR = American (Latino), EAS = East Asian, FIN = Finnish, NFE = Non-Finnish European, SAS = South Asian, SVK = Slovak. 2 7 SupplementaryTable 1 (uploaded as a separate Excel sheet of the Supplementary Table file):List of variants identified in the region of the CLCN1 (chloride voltage-gated channel 1, OMIM * 118425) gene in ExAC populations, dbSNP and in our data set. Only 17 of them had ExAC frequencies above 5% (highlighted in yellow). All but five were identified in our data set too with very similar calculated population frequencies. The exceptions, rs34904831, rs191902231, rs182668076, rs2280663 and rs73726622, were found to have ExAC frequencies +/-5% (depending on population). Originally three of these variants were identified in our data set too, although they were filtered out due slightly lower than 5% frequency (Suppl.Tab.1), further suggesting the feasibility of lowering our frequency restrictions. Our data contained also 89 variants missing from ExAC (highlighted in red), but found to have each of them deep intronic positions falling outside ExAC´s BED file. AFR = African/African American, AMR = American, EAS = East Asian, FIN = Finnish, NFE = Non-Finnish European, SAS = South Asian, SVK = Slovak. Supplementary Table 2 (uploaded as a separate Excel sheet of the Supplementary Table file): Verification of 87 positions in five polymorphic genomic loci of 58 randomly selected samples of our sample set from which genomic DNA was available to validation purposes. Reads from positions covered by multiple reads in individual samples (such in case of sample ID4730, where both alleles we...

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The future of DNA sequencing

Cited by 57 publications

References 9 publications

Targeted fetal cell‐free DNA screening for aneuploidies in 4,594 pregnancies: Single center study

Targeted fetal cell‐free DNA screening for aneuploidies in 4,594 pregnancies: Single center study

Biological explanations for discordant noninvasive prenatal test results: Preliminary data and lessons learned

Non-invasive prenatal testing as a valuable source of population specific allelic frequencies

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