Jan 11, 2017

Linked-Reads used in new NIPT approach

Shauna Clark

In a new publication entitled "Universal Haplotype-Based Noninvasive Prenatal Testing for Single Gene Diseases," researchers at the University of Hong Kong, along with collaborators, used 10x Technology to investigate the utility of Linked-Reads in the prenatal identification of single gene disorders.  Using noninvasive prenatal testing (NIPT), researchers were able to use a relative haplotype dosage (RHDO) methodology to make fetal diagnoses for 3 autosomal recessive disorders: congenital adrenal hyperplasia, β-thalassemia, Ellis-van Creveld syndrome and 2 X-linked disorders: Hemophilia and Hunter syndrome.

NIPT is primarily used for detecting fetal aneuploidy but has also been applied to the detection of single gene disorders.  Unlike aneuploidy detection, identification of single gene disorders using NIPT requires prior knowledge of the variant(s) and haplotypes contributing to disease.  The identification of maternally inherited alleles is the most difficult as maternal plasma generally only contains ~10% fetal DNA.  Determining whether the maternal disease-causing variant was inherited by the fetus is technically challenging if only a single variant is being assessed in this sample type.  The identification of phased SNPs near the disease-causing variant increases the power of the test, but generally requires access to DNA from another affected family member to identify the relevant haplotype.  Furthermore, due to meiotic recombination, the final, maternally-derived haplotype inherited by the fetus is a mosaic of the two original maternal haplotypes, and must be accounted for in the risk assessment.

In the study published by Hui et al., 10x Linked-Reads made the RHDO methodology possible by enabling phasing of maternal and paternal haplotypes using 10x-barcoded, next generation sequencing (NGS) short reads.  Researchers performed phased whole genome sequencing (WGS) or targeted sequencing of both parents and then targeted analysis of the fetal DNA based on the parental findings.  The final maternal haplotype, accounting for meiotic recombination, was deduced as a series of inheritance blocks from the two phased maternal haplotypes.  In 12 of the 13 families tested, the researchers were able to phase the locus of interest in both parents (or the maternal locus only for X-linked disorders), determine the RHDO in the fetus and make a fetal diagnosis, without the need for testing an affected family member to determine haplotypes.  Traditional prenatal diagnostic testing confirmed the diagnosis in all 12 cases.

Using a non-invasive approach, the authors have demonstrated that using a combination of 10x Linked-Reads to phase parental haplotypes and RHDO analysis of the fetal DNA is 100% effective in fetal diagnosis when single nucleotide polymorphism (SNP) zygosity is diverse.  Current testing for single gene disorders using NIPT samples often requires an affected family member, which may not be available for a variety of reasons.  Eliminating this need makes testing for single gene disorders more accessible.  Additionally, the 10x Linked-Read approach is superior to current digital droplet PCR (ddPCR) approaches as it does not require the use of probes, which can be difficult to design and require multiple rounds of revisions, the timing of which may not be fast enough to enable fetal diagnosis.  Another advantage of Linked-Reads is the ability to use NGS to get sequence and phasing information in traditionally difficult to access regions of the genome.

Additional Resources

See the full article here:

Universal Haplotype-Based Noninvasive Prenatal Testing for Single Gene Diseases
Hui et al., 2016. Clinical Chemistry PMID: 27932412