Proceedings

Variant Calling Pipeline Development to Detect Aneuploidy based on 100 SNPs from Illumina Sequencing

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Preimplantation genetic testing (PGT) is a process to prioritise in vitro fertilised embryos without
genetic defects for implantation. One of the conditions screened is aneuploidy. The genetic testing for
chromosomal aneuploidy ensures that all 23 pairs of chromosomes have the correct copy number.
The research utilized amplicon sequencing to generate sequence data and variant calling to produce
variant and coverage data to be analyzed by B-allele frequency (BAF) and copy number calculation for
aneuploidy and microdeletion and microduplication syndrome (MMS) assessment. The aim of the
bioinformatics study of this research is to develop the variant calling pipeline that is capable to detect
aneuploidy and MMS through BAF and copy number analysis. The research compares different
aligners and filter options through various analyses to establish the pipeline. Based on the analyses,
the final pipeline utilizes minimap2 with adapter trimming and with MAPQ30 filtering to generate high
quality variant and coverage data for aneuploidy and MMS detection.

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Availability

Detail Information

Series Title

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Call Number

BI 22-007

Publisher

i3L, Jakarta : i3L, Jakarta., 2022

Collation

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Language

English

ISBN/ISSN

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Classification

BI 22-007

Content Type

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Media Type

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Carrier Type

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Edition

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Subject(s)

Preimplantation Genetic Testing
PGT
B-allele frequency
microduplication syndrome

Specific Detail Info

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Statement of Responsibility

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