Science in Lab | A New Era of NIPT: Non-Invasive Prenatal Testing for Single Gene Disorders

DNA plays a crucial role in human growth and development. Irreparable DNA damage caused by external environmental factors leads to disease, which may be transmitted to future generations through genetic material. Common genetic disorders in humans can be divided into four broad categories: chromosomal, monogenic, polygenic, and mitochondrial disorders. While most single gene disorders are rare, their wide variety results in a cumulative overall incidence of 2% – 3%.


Prevention and Control of Single Gene Disorders 

The prevention and control of single-gene disorders takes place at three stages:

1. Preconception: Genetic counseling and PGT-M can help prevent and control genetic disorders. However, PGT-M is costly and complex, and prenatal diagnosis is generally still required after PGT-M.

2. Prenatal: For women with abnormal ultrasound or serum screening results, invasive prenatal diagnosis is still required (e.g., chorionic villus sampling, amniocentesis, cordocentesis), which is associated with approximately 1% risk of miscarriage.

3. Newborn: Newborn genetic screening is conducted after birth for early prevention.

Non-Invasive Prenatal Testing for Single Gene Disorders 

With advances in sequencing technology, researchers and healthcare professionals have identified ways to utilize cell-free fetal DNA in early screening of single gene disorders to facilitate early detection and intervention. A variety of techniques, including microarrays, digital PCR, RT-PCR, relative mutation dosage (RMD), relative haplotype dosage (RHDO) analysis, and high-throughput sequencing (NIPT-SGD), have been developed for early non-invasive screening of single gene disorders. RHDO analysis and NIPT-SGD perform well for de novo mutation detection as they do not rely on variant-specific testing.

RHDO analysis is a complex process that utilizes single nucleotide polymorphisms (SNPs) to phase the haplotypes of a proband and identify the maternal and paternal haplotypes linked with high-risk alleles. cfDNA sequencing data is then analyzed to phase fetal haplotypes and determine whether the fetus has inherited the high-risk allele. In contrast, NIPT-SGD directly interrogates key coding exons, introns, and intron/exon boundaries through targeted capture and NGS of the pregnant woman’s cfDNA. It is capable of detecting 1 – 100 disorders in a single test and does not require paternal genetic information, providing higher throughput and sensitivity than traditional tests.


Non-invasive prenatal testing (NIPT) and NIPT for single gene disorders (NIPT-SGD) both use cfDNA for testing, but there are differences in the methodologies they adopt. NIPT-SGD tests for mutations in exons, intron/exon boundaries, and important introns. The two commonly used tests, NIPT and NIPT Plus, are both based on low-depth whole-genome sequencing and are only capable of detecting chromosomal copy number abnormalities in the fetus. To detect smaller chromosomal microdeletions/microduplications, higher sequencing depth is required, which is usually achieved by targeted enrichment.


Non-invasive prenatal testing for single gene disorders




Disorders Tested

Dominant single-gene disorders


Aneuploidy, chromosomal microdeletions/microduplications

Number of Disorders Tested

1 – 100

T21, T18, T13



Targeted capture and high-throughput sequencing

Low-depth whole-genome sequencing

Low-depth whole-genome sequencing

Sequencing Depth

> 200×

~ 0.1×

~ 0.4×

Number of Reads

Usually > 20 M

Related to the number of probes and sequencing depth

3.5 – 5 M

15 – 25 M


Amniotic fluid test, first-generation sequencing

Mostly karyotyping

Karyotyping, CNV, CMA, etc.

Vazyme Products

Vazyme is committed to providing reliable materials for library preparation and capture reagents for our customers. By staying abreast of the latest advances in reproductive health, we assist in promoting prenatal and postnatal care.


Product Apply

Product Name

Cat. No

DNA extraction

cfDNA extraction

VAHTS Serum/Plasma Circulating DNA Kit


Library Prep

(for Illumina)

Enzymatic fragmentation DNA library preparation

VAHTS Universal Plus DNA Library Prep Kit for Illumina V2


Mechanical fragmentation DNA library preparation

VAHTS Universal DNA Library Prep Kit for Illumina V4


Library Prep

(for MGI)

Mechanical fragmentation DNA library preparation

VAHTS Universal DNA Library Prep Kit for MGI


Enzymatic fragmentation DNA Library Preparation

VAHTS Universal Plus DNA Library Prep Kit for MGI V2


Library Prep

(for Ion Torrent)

Mechanical fragmentation DNA library preparation

VAHTS Universal DNA Library Prep Kit for Ion Torrent V2


Targeted Capture

Multiplex Amplification Kit

VAHTS AmpSeq Library Prep Kit V3


Target Capture Hybridization and Wash Kit

VAHTS Target Capture Hybridization and Wash Kit


Capture Probe

VAHTS Target Capture Core Exome Panel


Target Capture Universal Blockers and Post-PCR Primer Mix

VAHTS Target Capture Universal Blockers and Post-PCR Primer Mix for Illumina-TS



Clean Beads

VAHTS DNA Clean Beads



1 × dsDNA HS Assay

Equalbit 1 × dsDNA HS Assay Kit



Adapter for Illumina

VAHTS Multiplex Oligos Set 4/Set 5 for Illumina


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