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Off the street phasing (OTSP): no hassle haplotype phasing for molecular PGD applications

  • David A. ZeeviEmail author
  • Fouad Zahdeh
  • Yehuda Kling
  • Shai Carmi
  • Gheona Altarescu
Genetics
  • 24 Downloads

Abstract

Purpose

Pre-implantation genetic diagnosis (PGD) for molecular disorders requires the construction of parental haplotypes. Classically, haplotype resolution (“phasing”) is obtained by genotyping multiple polymorphic markers in both parents and at least one additional relative. However, this process is time-consuming, and immediate family members are not always available. The recent availability of massive genomic data for many populations promises to eliminate the needs for developing family-specific assays and for recruiting additional family members. In this study, we aimed to validate population-assisted haplotype phasing for PGD.

Methods

Targeted sequencing of CFTR gene variants and ~ 1700 flanking polymorphic SNPs (± 2 Mb) was performed on 54 individuals from 12 PGD families of (a) Full Ashkenazi (FA; n = 16), (b) mixed Ashkenazi (MA; n = 23 individuals with at least one Ashkenazi and one non-Ashkenazi grandparents), or (c) non-Ashkenazi (NA; n = 15) descent. Heterozygous genotype calls in each individual were phased using various whole genome reference panels and appropriate computational models. All computationally derived haplotype predictions were benchmarked against trio-based phasing.

Results

Using the Ashkenazi reference panel, phasing of FA was highly accurate (99.4% ± 0.2% accuracy); phasing of MA was less accurate (95.4% ± 4.5% accuracy); and phasing of NA was predictably low (83.4% ± 6.6% accuracy). Strikingly, for founder mutation carriers, our haplotyping approach facilitated near perfect phasing accuracy (99.9% ± 0.1% and 98.2% ± 2.8% accuracy for W1282X and delF508 carriers, respectively).

Conclusions

Our results demonstrate the feasibility of replacing classical haplotype phasing with population-based phasing with uncompromised accuracy.

Keywords

PGD Haplotype phasing Population-based phasing Identity by descent CFTR 

Notes

Funding information

The authors thank the Shaare Zedek Mirsky intramural grant and Rabbi David Fuld for funding this research. S. C. thanks the Israel Science Foundation grant 407/17.

Compliance with ethical standards

All individuals agreed to use their DNA samples for this study, and ethical approval was obtained according to Shaare Zedek Medical Center institutional review board guidelines.

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Copyright information

© Springer Science+Business Media, LLC, part of Springer Nature 2019

Authors and Affiliations

  • David A. Zeevi
    • 1
    Email author
  • Fouad Zahdeh
    • 1
  • Yehuda Kling
    • 1
  • Shai Carmi
    • 2
  • Gheona Altarescu
    • 1
  1. 1.Medical Genetics InstituteShaare Zedek Medical Center (SZMC)JerusalemIsrael
  2. 2.Braun School of Public Health and Community MedicineThe Hebrew University of JerusalemJerusalemIsrael

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