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Karyotyping

Karyotyping

Evolutionary Relationships through Genome Comparisons

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Genome comparison is one of the excellent ways to interpret the evolutionary relationships between organisms. The basic principle of genome comparison is that if two species share a common feature, it is likely encoded by the DNA sequence conserved between both species. The advent of genome sequencing technologies in the late 20th century enabled scientists to understand the concept of conservation of domains between species and helped them to deduce evolutionary relationships across diverse...

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Sequencing of the human genome has opened up several best-kept secrets of the genome. Scientists have identified thousands of genome variations that exist within a population. These variations can be a single nucleotide or a larger chromosomal variation.
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Pre-Implantation Genetic Testing for Aneuploidy on a Semiconductor Based Next-Generation Sequencing Platform

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Published on: August 17, 2022

Comparative Analysis of Two NGS-Based Platforms for Product-of-Conception Karyotyping.

Yuri Murase¹, Yui Shichiri¹, Hidehito Inagaki¹

¹Division of Molecular Genetics, Center for Medical Science, Fujita Health University, 1-98 Dengakugakubo, Kutsukake-cho, Toyoake, Aichi 470-1192, Japan.

|August 29, 2024

Summary

This summary is machine-generated.

Low-coverage whole-genome sequencing (lcWGS) offers a viable alternative to traditional methods for analyzing product of conception (POC) chromosomal abnormalities. Both tested next-generation sequencing (NGS) systems provide equivalent diagnostic results for POC karyotyping.

Keywords:

NGS X chromosome karyotype methylation product of conception

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Pre-Implantation Genetic Testing for Aneuploidy on a Semiconductor Based Next-Generation Sequencing Platform

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Semiconductor Sequencing for Preimplantation Genetic Testing for Aneuploidy

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Published on: August 25, 2019

Area of Science:

Reproductive genetics
Genomics
Cytogenetics

Background:

Accurate cytogenetic analysis of product of conception (POC) is crucial for identifying chromosomal abnormalities, guiding genetic testing decisions.
Traditional G-banding microscopy for POC evaluation is prone to detection failures due to cell culture issues.
Low-coverage whole-genome sequencing (lcWGS) using next-generation sequencing (NGS) is emerging as a promising alternative for POC analysis.

Purpose of the Study:

To comparatively analyze two distinct NGS-based protocols for lcWGS in POC samples.
To evaluate the diagnostic equivalence of Illumina VeriSeq and Thermo Fisher ReproSeq systems for POC cytogenomic analysis.
To investigate discrepancies in X chromosome read counts observed in female POC samples.

Main Methods:

Comparative analysis of two short-read NGS platforms (Illumina VeriSeq/MiSeq and Thermo Fisher ReproSeq/Ion S5) for lcWGS.
Analysis of 20 product of conception (POC) samples.
Fluorescence in situ hybridization (FISH) analysis to rule out mosaicism.
Nanopore sequencing to assess DNA methylation status.

Main Results:

Both NGS-based lcWGS systems yielded equivalent cytogenomic diagnoses for all 20 POC samples.
Reduced X chromosome sequence reads were observed in some female samples, identified as a technical artifact related to X chromosome inactivation, not low-level mosaicism.
Nanopore sequencing confirmed predominant unmethylation in DNA samples exhibiting the X chromosome artifact.

Conclusions:

Both tested NGS systems for lcWGS are effective and comparable alternatives for POC karyotyping.
X chromosome data from these NGS methods requires careful interpretation due to potential artifacts linked to X chromosome inactivation.
Further validation is recommended, particularly concerning X chromosome analysis in female POC samples.