An alternative to array-based diagnostics: a prospectively recruited cohort, comparing arrayCGH to next-generation sequencing to evaluate foetal structural abnormalities

Walker, Lesley; Watson, Christopher M.; Hewitt, Sarah; Crinnion, Laura A.; Bonthron, David T.; Cohen, Kelly

doi:10.1080/01443615.2018.1522529

Cited by 6 publications

(12 citation statements)

References 23 publications

(17 reference statements)

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“…Molecular tools have made the reliable diagnosis of homogeneous chromosomal abnormalities on native DNA routine. In the future, broader accessibility of next generation sequencing-based analysis for invasive and non-invasive testing, combining point mutations, aneuploidy, and CNV analysis will probably make CMA obsolete [16,17]. But karyotyping and FISH on native and cultured cells is still a useful diagnostic complement, particularly in cases of com-…”

Section: Discussionmentioning

confidence: 99%

False Negative Results in Prenatal Aneuploidy Invasive Testing: Two Case Reports

Hamza¹,

Rachid²,

Levy³

et al. 2021

ACMCR

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Section: Discussionmentioning

confidence: 99%

False Negative Results in Prenatal Aneuploidy Invasive Testing: Two Case Reports

Hamza¹,

Rachid²,

Levy³

et al. 2021

ACMCR

View full text Add to dashboard Cite

“…NGS enables analysis of nucleotides variation (using WES) and study of CNVs 36 . Compared with hybridisation technology in CMA, NGS generates sequencing reads that are mapped on chromosomes and quantitatively counted and segmented into region of an equal copy number.…”

Section: Next Generation Sequencing For Cnv Analysismentioning

confidence: 99%

“…Low-pass WGS is most beneficial in terms of cost per sample, turnaround time, and sensitivity and resolution in CNV detection. Depending on the workflow, 6 to 28 million single end reads of 35 to 51 bp generated from each sample suffice for CNV analysis 36,37,40 . Such NGS-based analysis for CNV detection is referred to as CNV-seq 36,41 or low-pass (or low-coverage) WGS/ NGS 37,40 .…”

Section: Next Generation Sequencing For Cnv Analysismentioning

confidence: 99%

“…The NGS-based method can adjust the resolution by altering the number of samples processed within the batch: fewer samples in a batch increase read-count per sample, hence increasing the resolution of imbalances to be detected. The NGS-based method requires relatively low amount of starting genetic material of 100 to 200 ng 36,37 , depending on the sequencing platform and protocol. Low-pass NGS-based CNV analysis shares some of the limitations of CMA.…”

Section: Next Generation Sequencing For Cnv Analysismentioning

confidence: 99%

“…Low-pass NGS is a reliable and robust alternative for CNV analysis with shorter turnaround time, higher resolution, capable of detecting lower level of mosaicism (by scaling up the sequencing depth), and improved detection of CNV, compared with CMA. Its clinical utility in prenatal setting has been demonstrated in prospective studies 36,[42][43][44] . A large-scale prospective study in Mainland China involving 3429 women with amniocentesis reported detection of 2.83% pathogenic/likely pathogenic CNV, and 1.43% of variants of uncertain significance 43 .…”

Section: Next Generation Sequencing For Cnv Analysismentioning

confidence: 99%

See 2 more Smart Citations

Development of cytogenomics for prenatal diagnosis: from chromosomes to single nucleotides: a review

Chan

Kan

2019

Hong Kong Journal of Gynaecology, Obstetrics and Midwifery

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Prenatal diagnosis encompasses traditional cytogenetics and molecular-based techniques. In the new era of genomics, challenge to prenatal diagnosis has led to revised diagnostic strategies. In this review, we discuss the application of chromosomal microarray and a new prenatal diagnosis workflow in the public setting in Hong Kong. Using this prenatal diagnosis workflow, up to 40% of fetuses with structural anomalies can be identified with an underlying genetic aetiology, leaving the majority of cases undiagnosed. With the advancement of next generation sequencing, we are able to tackle the challenge of investigating chromosomal changes to single nucleotide variant level. Therefore, we also discuss whole exome sequencing, whole genome sequencing, and long-read sequencing, as well as their limitations and prenatal applications. This DNA-based technology should be evaluated for prenatal clinical application in Hong Kong.

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Application of Restriction Site-Associated DNA Sequencing (RAD-Seq) for Copy Number Variation and Triploidy Detection in Human

et al. 2021

Cytogenet Genome Res

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At present, low-pass whole-genome sequencing (WGS) is frequently used in clinical research and in the screening of copy number variations (CNVs). However, there are still some challenges in the detection of triploids. Restriction site-associated DNA sequencing (RAD-Seq) technology is a reduced-representation genome sequencing technology developed based on next-generation sequencing. Here, we verified whether RAD-Seq could be employed to detect CNVs and triploids. In this study, genomic DNA of 11 samples was extracted employing a routine method and used to build libraries. Five cell lines of known karyotypes and 6 triploid abortion tissue samples were included for RAD-Seq testing. The triploid samples were confirmed by STR analysis and also tested by low-pass WGS. The accuracy and efficiency of detecting CNVs and triploids by RAD-Seq were then assessed, compared with low-pass WGS. In our results, RAD-Seq detected 11 out of 11 (100%) chromosomal abnormalities, including 4 deletions and 1 aneuploidy in the purchased cell lines and all triploid samples. By contrast, these triploids were missed by low-pass WGS. Furthermore, RAD-Seq showed a higher resolution and more accurate allele frequency in the detection of triploids than low-pass WGS. Our study shows that, compared with low-pass WGS, RAD-Seq has relatively higher accuracy in CNV detection at a similar cost and is capable of identifying triploids. Therefore, the application of this technique in medical genetics has a significant potential value.

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An alternative to array-based diagnostics: a prospectively recruited cohort, comparing arrayCGH to next-generation sequencing to evaluate foetal structural abnormalities

Abstract: This is a repository copy of An alternative to array-based diagnostics: a prospectively recruited cohort, comparing arrayCGH to next-generation sequencing to evaluate foetal structural abnormalities.

Cited by 6 publications

References 23 publications

False Negative Results in Prenatal Aneuploidy Invasive Testing: Two Case Reports

False Negative Results in Prenatal Aneuploidy Invasive Testing: Two Case Reports

Development of cytogenomics for prenatal diagnosis: from chromosomes to single nucleotides: a review

Application of Restriction Site-Associated DNA Sequencing (RAD-Seq) for Copy Number Variation and Triploidy Detection in Human

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