scHaplotyper

scHaplotyper reconstructs and visualizes haplotype profiles from single-cell DNA sequencing data to support haplotype-based preimplantation genetic diagnosis (PGD) and carrier-status inference in IVF embryos.

Key Features:

• Haplotype Reconstruction: Uses a Hidden Markov Model (HMM) to infer haplotypes and determine chromosomal blocks inherited from parents for tracking disease allele transmission.
• WGA Artifact Handling: Employs HMM-based inference to manage complications introduced by whole genome amplification (WGA) artifacts in single-cell data.
• Visualization Capabilities: Produces detailed visual representations of haplotype profiles to trace the origin of haplotype blocks within embryos.
• Carrier Status Detection: Detects carrier status for specific disease alleles in embryos based on reconstructed haplotypes.
• NGS-Based Screening: Operates on Next Generation Sequencing (NGS) data to enable high-resolution genetic analysis of preimplantation embryos.

Scientific Applications:

• Preimplantation Genetic Diagnosis (PGD): Reconstructs embryo haplotypes to aid identification and selection of embryos with reduced risk of inheriting specific genetic disorders.
• Clinical Validation: Applied in clinical families affected by genetic disorders with reported successful application resulting in healthy live births of two children.

Methodology:

Applies a Hidden Markov Model (HMM) to interpret single-cell sequencing data and mitigate whole genome amplification (WGA) artifacts, using Next Generation Sequencing (NGS) data as input.