【佳學(xué)基因檢測】基因測序結(jié)果如何通過GENECODE/CCDS進行解碼檢測
當(dāng)前版本的 ANNOVAR 沒有為 GENCODE 提供特定的關(guān)鍵字,但 ANNOVAR 的通用性足以處理 GENCODE 或任何其他基因定義。 GENCODE 系統(tǒng)在過去幾年中發(fā)生了很大變化,賊新版本是 2014 年 2 月的 V19。在 V19 中,BASIC 軌道現(xiàn)已可用,其中包含基于以下描述的高質(zhì)量基因定義:“GENCODE Basic 該集旨在提供對大多數(shù)用戶有用的 GENCODE 轉(zhuǎn)錄本注釋的簡化子集。目標(biāo)是擁有一個覆蓋所有基因座的高質(zhì)量基本集。選擇 GENCODE 注釋以包含在基本集中 獨立確定每個基因位點的編碼和非編碼轉(zhuǎn)錄本。”
下面是基因解碼可以用于變異注釋的 GENCODE 基因定義的命令(請注意,如果 humandb/hg19_seq 中沒有全基因組 FASTA 文件,基因檢測與基因測序機構(gòu)應(yīng)該首先執(zhí)行 annotate_variation.pl -downdb -build hg19 seq humandb/hg19_seq/ )。
[jiaxuegene@genejiedu ~/]$ annotate_variation.pl -downdb wgEncodeGencodeBasicV19 humandb/ -build hg19
NOTICE: Web-based checking to see whether ANNOVAR new version is available ... Done
NOTICE: Downloading annotation database http://hgdownload.cse.ucsc.edu/goldenPath/hg19/database/wgEncodeGencodeBasicV19.txt.gz ... OK
NOTICE: Uncompressing downloaded files
NOTICE: Finished downloading annotation files for hg19 build version, with files saved at the 'humandb' directory
[jiaxuegene@genejiedu ~/]$ retrieve_seq_from_fasta.pl -format genericGene -seqdir humandb/hg19_seq/ -outfile humandb/hg19_wgEncodeGencodeBasicV19Mrna.fa humandb/hg19_wgEncodeGencodeBasicV19.txt
[jiaxuegene@genejiedu ~/]$ annotate_variation.pl -build hg19 -out ex1 -dbtype wgEncodeGencodeBasicV19 example/ex1.avinput humandb/
NOTICE: The --geneanno operation is set to ON by default
NOTICE: Reading gene annotation from humandb/hg19_wgEncodeGencodeBasicV19.txt ... Done with 95929 transcripts (including 38291 without coding sequence annotation) for 42594 unique genes
NOTICE: Reading FASTA sequences from humandb/hg19_wgEncodeGencodeBasicV19Mrna.fa ... Done with 16 sequences
WARNING: A total of 303 sequences will be ignored due to lack of correct ORF annotation
NOTICE: Finished gene-based annotation on 15 genetic variants in example/ex1.avinput
NOTICE: Output files were written to ex1.variant_function, ex1.exonic_variant_function
Then check the results below:
[[jiaxuegene@genejiedu ~/]$ cat ex1.variant_function
UTR5 ISG15(ENST00000379389.4:c.-33T>C) 1 948921 948921 T C comments: rs15842, a SNP in 5' UTR of ISG15
UTR3 ATAD3C(ENST00000378785.2:c.*91G>T) 1 1404001 1404001 G T comments: rs149123833, a SNP in 3' UTR of ATAD3C
splicing NPHP4(ENST00000378156.4:exon22:c.2818-2T>A) 1 5935162 5935162 A T comments: rs1287637, a splice site variant in NPHP4
intronic DDR2 1 162736463 162736463 C T comments: rs1000050, a SNP in Illumina SNP arrays
intronic DNASE2B 1 84875173 84875173 C T comments: rs6576700 or SNP_A-1780419, a SNP in Affymetrix SNP arrays
intergenic RP13-221M14.3(dist=46825),PRAMEF26(dist=5062) 1 13211293 13211294 TC - comments: rs59770105, a 2-bp deletion
intergenic UBIAD1(dist=48375),PTCHD2(dist=135699) 1 11403596 11403596 - AT comments: rs35561142, a 2-bp insertion
intergenic RP11-364B6.1(dist=872522),RP11-251P6.1(dist=652543) 1 105492231 105492231 A ATAAA comments: rs10552169, a block substitution
exonic IL23R 1 67705958 67705958 G A comments: rs11209026 (R381Q), a SNP in IL23R associated with Crohn's disease
exonic ATG16L1 2 234183368 234183368 A G comments: rs2241880 (T300A), a SNP in the ATG16L1 associated with Crohn's disease
exonic NOD2 16 50745926 50745926 C T comments: rs2066844 (R702W), a non-synonymous SNP in NOD2
exonic NOD2 16 50756540 50756540 G C comments: rs2066845 (G908R), a non-synonymous SNP in NOD2
exonic NOD2 16 50763778 50763778 - C comments: rs2066847 (c.3016_3017insC), a frameshift SNP in NOD2
exonic GJB2 13 20763686 20763686 G - comments: rs1801002 (del35G), a frameshift mutation in GJB2, associated with hearing loss
exonic CRYL1,GJB6 13 20797176 21105944 0 - comments: a 342kb deletion encompassing GJB6, associated with hearing loss
[jiaxuegene@genejiedu ~/]$ cat ex1.exonic_variant_function
line9 nonsynonymous SNV IL23R:ENST00000395227.1:exon4:c.G377A:p.R126Q,IL23R:ENST00000347310.5:exon9:c.G1142A:p.R381Q, 1 67705958 6770595comments: rs11209026 (R381Q), a SNP in IL23R associated with Crohn's disease
line10 nonsynonymous SNV ATG16L1:ENST00000373525.5:exon6:c.A466G:p.T156A,ATG16L1:ENST00000347464.5:exon5:c.A409G:p.T137A,ATG16L1:ENST00000392018.1:exon10:c.A949G:p.T317A,ATG16L1:ENST00000392017.4:exon9:c.A898G:p.T300A,ATG16L1:ENST00000392020.4:exon8:c.A841G:p.T281A, 2 234183368 234183368 comments: rs2241880 (T300A), a SNP in the ATG16L1 associated with Crohn's disease
line11 nonsynonymous SNV NOD2:ENST00000300589.2:exon4:c.C2104T:p.R702W, 16 50745926 50745926 C T comments: rs2066844 (R702W), a non-synonymous SNP in NOD2
line12 nonsynonymous SNV NOD2:ENST00000300589.2:exon8:c.G2722C:p.G908R, 16 50756540 50756540 G C comments: rs2066845 (G908R), a non-synonymous SNP in NOD2
line13 frameshift insertion NOD2:ENST00000300589.2:exon11:c.3017dupC:p.A1006fs, 16 50763778 50763778 - C comments: rs2066847 (c.3016_3017insC), a frameshift SNP in NOD2
line14 frameshift deletion GJB2:ENST00000382848.4:exon2:c.35delG:p.G12fs,GJB2:ENST00000382844.1:exon1:c.35delG:p.G12fs, 13 20763686 2076368comments: rs1801002 (del35G), a frameshift mutation in GJB2, associated with hearing loss
line15 frameshift deletion GJB6:ENST00000241124.6:wholegene,CRYL1:ENST00000298248.7:wholegene,GJB6:ENST00000400065.3:wholegene,CRYL1:ENST00000382812.1:wholegene,GJB6:ENST00000356192.6:wholegene,GJB6:ENST00000400066.3:wholegene, 13 20797176 21105944 0 - comments: a 342kb deletion encompassing GJB6, associated with hearing loss
同樣,基因解碼可以使用不同的 -dbtype 參數(shù)(wgEncodeGencodeCompV19 和 wgEncodeGencodePolyaV19)切換到 GENCODE 的綜合注釋和 PolyA 注釋。
使用這些注釋時,務(wù)必注意要使用的正確文件名(如果您不確定表名,請使用 UCSC 基因組瀏覽器中的表瀏覽器)。
還支持許多其他基因定義系統(tǒng)。 例如,用戶可以選擇CCDS基因定義。 (請注意,如果 humandb/hg19_seq 中沒有全基因組 FASTA 文件,獲得基因序列后應(yīng)該首先執(zhí)行 annotate_variation.pl -downdb -build hg19 seq humandb/hg19_seq/)。
[jiaxuegene@genejiedu ~/]$ annotate_variation.pl -downdb -build hg19 ccdsGene humandb
[jiaxuegene@genejiedu ~/]$ retrieve_seq_from_fasta.pl humandb/hg19_ccdsGene.txt -seqdir humandb/hg19_seq -format refGene -outfile humandb/hg19_ccdsGeneMrna.fa
[jiaxuegene@genejiedu ~/]$ annotate_variation.pl -buildver hg19 -out ex1 -dbtype ccdsGene example/ex1.avinput humandb/
NOTICE: The --geneanno operation is set to ON by default
NOTICE: Reading gene annotation from humandb/hg19_ccdsGene.txt ... Done with 29045 transcripts (including 0 without coding sequence annotation) for 29014 unique genes
NOTICE: Reading FASTA sequences from humandb/hg19_ccdsGeneMrna.fa ... Done with 8 sequences
WARNING: A total of 38 sequences will be ignored due to lack of correct ORF annotation
NOTICE: Finished gene-based annotation on 15 genetic variants in example/ex1.avinput
NOTICE: Output files were written to ex1.variant_function, ex1.exonic_variant_functiona
基因解碼技術(shù)解釋:對于 CCDS 基因,輸出將不包含基因名稱,而僅包含 CCDS 標(biāo)識符。 要獲取基因名稱,基因檢測機構(gòu)必須編寫自己的程序來處理 ANNOVAR 輸出文件。 有兩個表可用于將 CCDS ID 轉(zhuǎn)換為其他 ID:ccdsNotes 將 CCDS 轉(zhuǎn)換為 UCSC 已知基因轉(zhuǎn)錄本 ID,然后您可以將其轉(zhuǎn)換為基因名稱。 ccdsInfo 表將 CCDS ID 轉(zhuǎn)換為 ENSEMBL 轉(zhuǎn)錄本或 RefSeq 轉(zhuǎn)錄本,然后您可以進一步將它們轉(zhuǎn)換為基因名稱。