Perspective on the technical challenges involved in the implementation of array-CGH in prenatal diagnostic testing

Prenatal diagnosis: the clinical usefulness of array comparative genomic hybridization

Background

Array comparative genomic hybridization (aCGH) has been replacing karyotype in neurodevelopment diseases or intellectual disability cases. Regarding prenatal diagnosis (PND) karyotyping is still the criterion standard technique; nevertheless, the application of aCGH in this field has been increasing dramatically and some groups recommended it as the first-tier prenatal genetic test in cases of fetal ultrasound abnormalities. Despite aCGH greater resolution, the detection of variants of unknown significance (VOUS) is not desirable, so it's need some reflexion before generalized application on PND.

Objective

The aim of this study was to analyze the prevalence and type of copy number variants (CNVs) detected in the 55 PND samples collected from pregnancies with indication to perform aCGH.

Methods

aCGH was performed using Agilent 4 × 180K microarrays and results were analyzed using CytoGenomics software.

Results and conclusion

Eight (14.5%) cases had pathogenic or likely pathogenic CNVs. VOUS were found in 21.8% of the cases, but this frequency could be minimized if only large CNVs above 1 million base pairs that are outside the clinically curated targeted regions were considered.

Genome-Wide Transcriptional Excavation of Dipsacus asperoides Unmasked both Cryptic Asperosaponin Biosynthetic Genes and SSR Markers

BACKGROUND

Dipsacus asperoides is a traditional Chinese medicinal crop. The root is generally used as a medicine and is frequently prescribed by Chinese doctors for the treatment of back pain, limb paralysis, flutter trauma, tendon injuries, and fractures. With the rapid development of bioinformatics, research has been focused on this species at the gene or molecular level. For purpose of fleshing out genome information about D. asperoides, in this paper we conducted transcriptome analysis of this species.

PRINCIPAL FINDINGS

To date, many genes encoding enzymes involved in the biosynthesis of triterpenoid saponins in D.asperoides have not been elucidated. Illumina paired-end sequencing was employed to probe D. asperoides's various enzymes associated with the relevant mesostate. A total of 30, 832,805 clean reads and de novo spliced 43,243 unigenes were obtained. Of all unigenes, only 8.27% (3578) were successfully annotated in total of seven public databases: Nr, Nt, Swiss-Prot, GO, KOG, KEGG, and Pfam, which might be attributed to the poor studies on D. asperoides. The candidate genes encoding enzymes involved in triterpenoid saponin biosynthesis were identified and experimentally verified by reverse transcription qPCR, encompassing nine cytochrome P450s and 17 UDP-glucosyltransferases. Specifically, unearthly putative genes involved in the glycosylation of hederagenin were acquired. Simultaneously, 4490 SSRs from 43,243 examined sequences were determined via bioinformatics analysis.

CONCLUSION

This study represents the first report on the use of the Illumina sequence platform on this crop at the transcriptome level. Our findings of candidate genes encoding enzymes involved in Dipsacus saponin VI biosynthes is provide novel information in efforts to further understand the triterpenoid metabolic pathway on this species. The initial genetics resources in this study will contribute significantly to the genetic breeding program of D. asperoides, and are beneficial for clinical diagnosis and treatment.

Prenatal diagnosis of single gene disorders using amniotic fluid as the starting material for PCR

A rapid and inexpensive method for fetal genetic diagnosis using amniotic fluid (AF) as the starting material was demonstrated in this study.