LAMPS: an analysis pipeline for sequence-specific ligation-mediated amplification reads

Abstract

Objective: Ligation-Mediated Amplification (LMA) is a versatile biochemical tool for amplifying selected DNA sequences. LMA has increased in popularity due to its integration within chromosome conformation capture (5C) and chromatin immunoprecipitation (2C-ChIP) methodologies. The output of either 5C or 2C-ChIP protocols is a single-read sequencing library of ligated primer pairs that may or may not be multiplexed. While many computational tools currently exist for read mapping and analysis, these tools neither fully support multiplexed libraries nor provide qualitative reporting on the LMA primers involved. Typically, the task of library demultiplexing or primer analysis is offloaded on to the user. Our aim was to develop an easy-to-use pipeline for processing (multiplexed) single-read sequencing data produced by sequence-specific LMA. Results: Here, we describe the Ligation-mediated Amplified, Multiplexed Primer-pair Sequence (LAMPS) analysis pipeline. LAMPS facilitates the analysis of multiplexed LMA sequencing data and provides a thorough assessment of a library's reads for a variety of experimental parameters (e.g., primer-pair efficiency). The standardized output of LAMPS allows for easy integration with downstream analyses, such as data track visualization on a genome browser.

3D genome organization and epigenetic regulation in autoimmune diseases

“…5C uses a highly multiplexed ligation-mediated amplification that allows the amplification of 3C ligation compounds. Either microarray or high-throughput DNA sequencing is used to examine the resulting 5C library of ligated primers ( 51 ). As the many-to-many technique, 5C has been applied to 1% of the human genome to explore long-range interactions between DNA sequences and distal regulators ( 52 ).…”