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Chemistry is the study of matter and the changes it undergoes. Matter is anything that has mass and occupies space. Matter is all around us; the air, water, soil, mountains, even our bodies are all examples of matter. Matter is divided into three states — solid, liquid, and gas — that are commonly found on earth. The fourth state of matter, plasma, occurs naturally in the interiors of stars. 
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Related Experiment Video

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Stability and Structure of Bat Major Histocompatibility Complex Class I with Heterologous β2-Microglobulin
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Genotyping strategy matters when analyzing hypervariable major histocompatibility complex-Experience from a passerine

Silje L Rekdal1, Jarl Andreas Anmarkrud1, Arild Johnsen1

  • 1Natural History Museum University of Oslo Oslo Norway.

Ecology and Evolution
|February 14, 2018
PubMed
Summary
This summary is machine-generated.

Genotyping highly variable MHC genes in bluethroats is complex. Different high-throughput methods yield inconsistent results for MHC class II exon 2 due to PCR biases, highlighting allelic dropout challenges.

Keywords:
Illumina MiSeqIon TorrentLuscinia svecicabluethroatmajor histocompatibility complex

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Area of Science:

  • * Genomics and immunology, focusing on the Major Histocompatibility Complex (MHC).
  • * Avian genetics and population studies, specifically in *Luscinia svecica* (bluethroat).

Background:

  • * Major Histocompatibility Complex (MHC) genes are crucial for immune response but are challenging to genotype due to high variability and copy number.
  • * Accurate genotyping of MHC loci is essential for understanding immune diversity and adaptation in wild populations.

Purpose of the Study:

  • * To evaluate different high-throughput sequencing strategies for genotyping MHC class I exon 3 (MHCIe3) and MHC class II exon 2 (MHCIIβe2) in bluethroats.
  • * To assess the consistency and identify potential biases across various genotyping approaches for hypervariable MHC regions.

Main Methods:

  • * Sequencing of two bluethroat family groups (eight individuals) using Ion Torrent and Illumina MiSeq platforms.
  • * Application of modified Sommer pipeline and AmpliSAS software for allele calling.
  • * Utilized single- and dual-indexed primer structures for Ion Torrent sequencing.

Main Results:

  • * MHCIe3 genotyping yielded consistent results, with up to eight alleles per individual.
  • * MHCIIβe2 genotyping revealed significant complexity, with up to 56 alleles per individual, and substantial allelic dropout (18-50%) across methods.
  • * Discrepancies in MHCIIβe2 allele detection were linked to PCR biases and platform-specific primer tails, with AmpliSAS calling fewer alleles than the modified Sommer pipeline.

Conclusions:

  • * Allelic dropout is a major challenge in genotyping hypervariable MHCIIβe2, with method-specific biases affecting results.
  • * Direct comparison of genotypes across different sequencing strategies is cautioned due to non-random error patterns.
  • * Despite limitations, high-throughput sequencing advances MHC genotyping, though complete allelic repertoire may not be captured.