Whole Genome Sequencing: The Way Forward for Molecular Cytogenetics
Gayatri N, Surya Prabha B, Prajnya Ranganath Department of Medical Genetics, Nizam’s Institute of Medical Sciences, Hyderabad Correspondence to: Dr Prajnya RanganathEmail:prajnyaranganath@gmail.com
1 Utility of NGS in Prenatally Detected Balanced Chromosomal Rearrangements (Halgren et al., 2018)
Prenatally detected de novo balanced chromosomal rearrangements have been reported to be associated with a 6-9% risk
of adverse outcome, but the postnatal long-term morbidity in these antenatally detected cases has not been adequately
studied. In this study, Halgren et al. have obtained long term follow-up data, for a mean period of around 17 years, from
an existing national registry as well as through clinical follow-up, for 41 individuals who had prenatally detected de novo
apparently balanced chromosomal rearrangements (BCRs) but no antenatal ultrasound anomalies (where the pregnancy
was continued), and found that as many as 27% of them developed neuropsychiatric or neurodevelopmental disorders.
Samples could be obtained from 32 out of these 41 individuals. Chromosomal microarray (CMA) in all these
32 cases was normal. Next generation sequencing (NGS)-based mate-pair sequencing could be done in 29
cases, out of which 21 had intragenic or non-genic disruptions. The findings included disruption of genes
(ARID1B, NPAS3, CELF4) or regulatory domains of known developmental genes (ZEB2, HOXC), or complex
BCRs which correlated with the adverse outcomes in these patients. This study demonstrates that NGS
outperforms CMA in the characterization of prenatally detected de novo BCRs and can help in more accurate
prognostication of these cases. NGS-based mate pair sequencing may soon replace CMA in the evaluation of de novo
BCRs, specifically in cases with structurally normal fetuses, where the diagnostic yield of CMA is very
low.
2 Utility of WGS in Copy Number Variation Analysis (Zhou et al., 2018)
Conventionally, sequencing technologies have been stated to be unsuitable for identification of copy number variations
(CNVs), and molecular cytogenetic techniques especially chromosomal microarray (CMA) have been recommended for
CNV analysis. In their study, Zhou et al. have studied the ability of three Whole Genome Sequencing (WGS) strategies -
short insert, 3 kb insert mate pair and 5 kb insert mate pair (each at 1X, 3X and 5X coverages) to detect CNVs. They
have investigated how these strategies perform relative to each other and also compared their yield to 17 currently used
high-density oligonucleotide arrays. A set of gold standard CNVs generated for the 1000 Genomes Project
(CEU subject NA12878) was used as the benchmark. WGS strategies with even low coverage were found to
be able to detect significantly more CNVs and gold standard CNVs with validation, when compared to
the high-density oligonucleotide array platforms. Thus, WGS appears to be having a higher sensitivity
than even the best performing arrays, in detecting CNVs, with a lower percentage of unvalidated CNV
calls.
3 WGS-based NIPT for Prenatal Cytogenetic Analysis (Van Opstal et al., 2018)
A new study from Netherlands by Van Opstal et al. has reported the yield of Whole Genome Sequencing (WGS)- based
non-invasive prenatal testing (NIPT) for the detection of chromosomal aberrations other than common
chromosomal aneuploidies, among participants of the TRIDENT study (Trial by Dutch laboratories for Evaluation
of Non-invasive prenatal Testing). Out of the 2527 cases where whole-genome shallow massively parallel
shotgun sequencing was performed in the cell-free DNA derived from the maternal blood sample, in 78,
one of the common trisomies was reported (trisomy 21/13/18) and in 41 (1.6%), some other chromosomal
aberration was found. Further cytogenetic evaluation of the chorionic villi/ amniotic fluid/ fetal blood/ fetal
skin/ placental samples revealed that out of these 41 chromosomal aberrations detected through NIPT, 10
were fetal, 22 were placental and 1 was a maternal CNV; in 7 cases, the origin of the aberration remained
unresolved and in one case, cytogenetic follow-up could not be done. Nine of the 10 fetal chromosomal
aberrations were associated with an abnormal clinical phenotype and 13 of the 22 placental aberrations
were associated with fetal congenital anomalies and/or poor fetal growth. This study demonstrates the
utility of WGS-based NIPT in the detection of chromosomal aberrations other than common trisomies and
also in the identification of confined placental chromosomal aberrations that may affect the pregnancy
outcome.
4 WGS as the First-tier Genetic Test for Pediatric Patients (Lionel et al., 2018)
The utility of Whole-genome sequencing (WGS) as a comprehensive testing platform in suspected pediatric genetic
disorders was explored in a study by Lionel et al. One hundred and three patients with a clinical phenotype suggestive of
an underlying genetic disorder were recruited from pediatric non-genetic subspecialty clinics. The diagnostic yield was
compared with that of conventional step-wise genetic testing. Diagnostic variants were identified in 41% of cases. WGS
was able to detect all the molecular aberrations detected by conventional genetic testing methods as well as an additional
18 variants, including structural and non-exonic sequence variants. WGS was thus shown to provide a higher
diagnostic yield as a primary test, when compared to conventional genetic tests, in a clinically heterogeneous
cohort.
References
1. Halgren C, et al. Risks and Recommendations in Prenatally Detected De Novo Balanced Chromosomal
Rearrangements from Assessment of Long-Term Outcomes. Am J Hum Genet 2018; 102: 1090-1103.
2. Lionel AC, et al. Improved diagnostic yield compared with targeted gene sequencing panels suggests a role
for whole-genome sequencing as a first-tier genetic test. Genet Med 2018; 20: 435-443.
3. Van Opstal D, et al. Origin and clinical relevance of chromosomal aberrations other than the common
trisomies detected by genome-wide NIPS: results of the TRIDENT study. Genet Med 2018; 20: 480-485.
4. Zhou B, et al. Whole-genome sequencing analysis of CNV using low-coverage and paired-end strategies is
efficient and outperforms array-based CNV analysis. J Med Genet 2018; doi: 10.1136/jmedgenet-2018-105272.
[Epub ahead of print]