Amino Acid Conservation

Overview

Amino Acid Conservation scores are obtained from multiple alignments of vertebrate exomes to the human ones. The score indicate the frequency with which a particular AA is observed in Humans.

Publication

Siepel A, Bejerano G, Pedersen JS, Hinrichs AS, Hou M, Rosenbloom K, Clawson H, Spieth J, Hillier LW, Richards S, et al. Evolutionarily conserved elements in vertebrate, insect, worm, and yeast genomes. Genome Res. 2005 Aug;15(8):1034-50. (http://www.genome.org/cgi/doi/10.1101/gr.3715005)

FASTA File

The exon alignments are provided in FASTA files as follows:

>ENST00000641515.2_hg38_1_2 3 0 0 chr1:65565-65573+
MKK
>ENST00000641515.2_panTro4_1_2 3 0 0 chrUn_GL393541:146907-146915+
MKK
>ENST00000641515.2_gorGor3_1_2 3 0 0
---
>ENST00000641515.2_ponAbe2_1_2 3 0 0 chr15:99141417-99141425-
MKK
>ENST00000641515.2_hg38_2_2 324 0 0 chr1:69037-70008+
VTAEAISWNESTSETNNSMVTEFIFLGLSDSQELQTFLFMLFFVFYGGIVFGNLLIVITVVSDSHLHSPMYFLLANLSLIDLSLSSVTAPKMITDFFSQRKVISFKGCLVQIFLLHFFGGSEMVILIAMGFDRYIAICKPLHYTTIMCGNACVGIMAVTWGIGFLHSVSQLAFAVHLLFCGPNEVDSFYCDLPRVIKLACTDTYRLDIMVIANSGVLTVCSFVLLIISYTIILMTIQHRPLDKSSKALSTLTAHITVVLLFFGPCVFIYAWPFPIKSLDKFLAVFYSVITPLLNPIIYTLRNKDMKTAIRQLRKWDAHSSVKFZ
>ENST00000641515.2_panTro4_2_2 324 0 0 chrUn_GL393541:151333-152303+

Parsing FASTA

For each Ensembl transcript, we will need to aggregate all the exons together for each of the 100 species. From there, we should get a full alignment that can be used to determine conservation. For example, for ENST00000641515.2 we have:

Human (hg38) MKKVTAEAISWNESTSETNNSMVTEFIFLGLSDSQELQTFLFMLFFVFYGGIVFGNLLIVITVVSDSHLHSPMYFLLANLSLIDLSLSSVTAPKMITDFFSQRKVISFKGCLVQIFLL
Chimp        MKKVTAEAISWNESTSETNNSMVTEFIFLGLSDSQELQTFL-MLFFVFYGGIVFGNLLIVRIVVSDSHLHSPMYFLLANLSLIDLSLCSVTAPKMITDFFSQRKVISFKGCLVQIFLL
Gorilla      ----------------------------------------------------------------------------------------------------------------------
Orangutan    MKKVTAEAISWNESTSKTNNSVVTEFIFLGLSDSQELQTFLFMLFFVFYGGIVFGNLLIVIIVVSDSHLHSPMYFLLANLSLIDLSLSSVTAPKMITDFFSQRKVISFKGCLVQIFLL
Gibbon       ----------------------------------------------------------------------------------------------------------------------
Rhesus       MKKVTEAAISWNESTSETNNSIVTEFIFLGLSDSQELQIFLFVLFLVFYGGIVFGNLLIVITVVSDSHLHSPMYLLLANLSVVDLSLSSVTAPKMITDFFSQRKAISFKGCLVQIFLL
Macaque      MKKVTEAAISWNESTSETNNSIVTEFIFLGLSDSQELQIFLFVLFLVFYGGIVFGNLLIVITVVSDSHLHSPMYLLLANLSVIDLSLSSVTAPKMITDFFSQRKAISFKGCLVQIFLL

If we look at position 6, we see that humans have an Alanine (A) residue. This residue is shared by Chimp and Orangutan. However, Rhesus and Macaque have a Glutamic acid (E) residue at that position. Moreover, Gorilla and Gibbon don't even have data for that transcript. For position 6, we would say that we have 43% conservation (3/7) since three organisms share the same residue as humans.

Assigning scores to Illumina Connected Annotations transcripts

The source FASTA file comes with Ensembl/UCSC transcript ids of the transcripts used for alignments. The Illumina Connected Annotations cache has RefSeq and Ensembl transcripts and our first attempt was to map the given Ensembl/UCSC ids to their equivalent RefSeq/Ensembl ids. This attempt was unsuccessful since UCSC Table Browser provided mapping without version numbers. So we proceeded as follows:

• Take proteins which have a unique mapping (and hence one set of conservation scores). For ones that mapped to both ChrX and ChrY, we accepted the one from ChrX.
• A Illumina Connected Annotations transcript having an exact peptide sequence match with a uniquely aligned protein is assigned the corresponding conservation scores.

Unfortunately this left us with a very small number of transcripts having conservation scores.

GRCh37

• Source FASTA contained 41957 protein alignments.
• 38165 proteins had unique scores.
• 88 aligned proteins existed in Illumina Connected Annotations cache.
• 118 transcripts had conservation scores.

GRCh38

• Source FASTA contained 110024 protein alignments.
• 88961 proteins had unique scores.
• 11688 aligned proteins existed in Illumina Connected Annotations cache.
• 12098 transcripts had conservation scores.

Download URL

GRCh37: http://hgdownload.soe.ucsc.edu/goldenPath/hg19/multiz100way/alignments/knownGene.exonAA.fa.gz

GRCh38: http://hgdownload.soe.ucsc.edu/goldenPath/hg38/multiz100way/alignments/knownGene.exonAA.fa.gz

JSON Output

Conservation scores are reported in the transcript section. One score is reported for each alt allele

"aminoAcidConservation": {
    "scores": [0.34]
}  

Field	Type	Notes
aminoAcidConservation	object
scores	object array of doubles	percent conserved with respect to human amino acid residue. Range: 0.01 - 1.00