Pipeline

Due to the comparably low cost of NGS, use of this technology shifts efforts from data acquisition toward processing, analysis, and interpretation. Innumerable methods are available for these purposes, but several design patterns are common. This pipeline is an initial attempt to integrate necessary components into an automatable NGS processing workflow, which can be applied the human major histocompatibility complex (MHC), a region that represents significant human genetic variation with broad research and clinical application.

The workflow includes all necessary components for its execution, including IT infrastructure and hardware (cloud); development and test environment; application programming interfaces, tools and software; reference databases and documentation for producing HML from raw sequencing reads.

Purpose

A simple workflow to generate research-grade consensus sequences from high-throughput (next-generation) DNA sequencing of individual or multiplexed, clonally-amplified genes representing the MHC, including human leukocyte antigen (HLA)-A, -B, -C, -DQB1, -DPB1, and -DRB1 as well as killer-cell immunoglobulin-like receptor (KIR).

All documentation and code referenced therein are intended for NON-CLINICAL RESEARCH USE ONLY.

Scope

The pipeline is designed to enable processing of targeted HLA NGS with the intent of further open source development to allow processing of additional genomic regions such as ABO/Rh, other targeted gene systems, whole-exomes or whole-genomes with paired or unpaired data from multiple sequencing platforms (Sanger, Illumina, Pacific Biosciences, Oxford Nanopore, Ion Torrent, or combinations thereof) and diverse applications (research, donor recruitment typing, clinical diagnostics, etc). Where specific parameters, filtering criteria, software or hardware configurations appear to overfit the pipeline to targeted HLA NGS the NMDP will document and disclose as release notes.

The pipeline represents what we consider to be a minimally viable workflow for generating consensus DNA sequence and interpretable alleles. Further details are provided in the methods or you can get started with a tutorial.