SNP microarray for amniocentesis

Description

GGA Prenatal SNP (single nucleotide polymorphism) microarray is a genetic testing that can be performed with amniocentesis. It is a type of DNA array which is designed with high density (copy number variation) CNV+SNP probes to detect small variations across the whole chromosome set. The detection rate for fetal chromosomal abnormalities is higher than karyotyping (G-banding) and traditional oligo-microarray.

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Overview

GGA Prenatal SNP microarray

Chromosomal abnormalities cause problems

Small chromosomal variations can lead to excess or shortage of genes within that region, thus resulting in a person with medical problems, such as abnormal growth, development, and abnormal function of the body’s systems. Chromosome numeral or structural variants can result in a person with disorders such as Down syndrome, Prader-Willi syndrome, and DiGeorge syndrome. Pregnancy at an advanced age increases the fetal risk of chromosomal abnormality.

Primary prenatal diagnostic test for fetal ultrasound abnormalities and abnormal screening result.

SNP microarray has been established as a useful diagnostic tool in pregnancy to detect fetal chromosomal abnormality. It could detect more chromosomal abnormalities than other existing testing methods and provides a more comprehensive genetic information of the fetus.

When to consider Prenatal SNP microarray?

The American College of Obstetricians and Gynecologists (ACOG) and the Society for Maternal-Fetal Medicine (SMFM) recommend that all pregnant women should be offered prenatal assessment for aneuploidy by screening or diagnostic testing regardless of maternal age or other risk factors. (Reference: Obstet Gynecol 2016;127:e108-22.)

It is recommended for pregnant women who:

desires definitive and comprehensive information about fetus.
have a family history of congenital anomalies or a previous pregnancy with a fetus with chromosomal abnormalities.
have abnormal prenatal findings from ultrasound scans, karyotype, and other screening tests (e.g. NIPT, First/Second-trimester maternal serum Down Syndrome screening).
Non-invasive Prenatal Test (NIPT) showing no-call or inconclusive results due to low fetal fraction.
carries multiple gestations.
achieved pregnancy by Preimplantation Genetic Testing for Aneuploidy (PGT-A).

Sample Requirements:

Amniotic fluid: 10-15mL
*Other sample requirements (CVS or DNA) can be discussed further

Features

GGA Prenatal SNP microarray with both CNV and SNP markers could identify genomic copy number changes and homozygosity, such as Absence of Heterozygosity (AOH), Uniparental Disomy (UPD), and triploidy, to help determine the genetic causes of abnormal findings and/or abnormal screening result.

Why choose GGA Prenatal SNP microarray?

Combines copy number markers with SNP markers at a high density to provide the highest resolution and coverage.
Able to detect more chromosomal abnormalities such as AOH, UPD and triploidy in one test.
Provide comprehensive genetic counseling support to clinicians.
CAP-accredited laboratory with over 12 years of experience in genetic testing.
GGA clinical studies^ yield a rich collection of genetic and clinical data on SNP microarray.

^References:

J FORMOS MED ASSOC. Mar 2019, 118(3), 739-742
Pediatrics and Neonatology. (2020) 61, 343-345
Acta Obstet Gynecol Scand. 2020 Jun;99(6):775-782.

Frequently asked questions

What is SNP microarray?

SNP Microarray is an efficient test with both Copy Number Variations (CNV) and Single
Nucleotide Polymorphism (SNP) markers that could identify numerical and large segmental chromosomal changes, microdeletions/ microduplications, and homozygosity to help determine the genetic causes of abnormal findings and/or abnormal screening results.

When should I use SNP microarray for Amniocentesis?

It is recommended for pregnant women who:

desires definitive and comprehensive information about fetus.
have a family history of congenital anomalies or a previous pregnancy with a fetus with chromosomal abnormalities.
have abnormal prenatal findings from ultrasound scans, karyotype, and other screening tests (e.g. NIPT, First/Second-trimester maternal serum Down Syndrome screening).
Non-invasive Prenatal Test (NIPT) showing no-call or inconclusive results due to low fetal fraction.
carries multiple gestations.
achieved pregnancy by Preimplantation Genetic Testing for Aneuploidy (PGT-A).

What is the main advantages of SNP microarray when compared to low pass whole genome sequencing for prenatal testing?

GGA SNP microarray contains a combination of copy number and SNP probes. This allows detection of uniparental disomy (UPD) and Loss of heterozygosity (LOH) as well as copy number changes and mosaic events. In low pass whole genome sequencing also called CNV-Seq there will be no information on SNPs, meaning you will miss any instances of UPD or LOH which may have a serious impact to the health of a child. Therefore the use of the GGA SNP microarray provides more information than with current CNV-Seq methods.

The use of CNV-Seq or other whole genome sequencing approaches to our knowledge, is not currently recommended by any of the main societies, whereas microarray is generally recommended as the first-tier test when invasive prenatal testing is involved and is an excellent tool to complement or confirm other non-invasive approaches.

How long does it take to receive the result of SNP microarray?

SNP Microarray has an average turn-around-time of 7-10 working days.