【广东会GDH基因检测】基因测序结果如何通过GENECODE/CCDS进行解码检测
当前版本的 ANNOVAR 没有为 GENCODE 提供特定的关键字，但 ANNOVAR 的通用性足以处理 GENCODE 或任何其他基因定义。 GENCODE 系统在过去几年中发生了很大变化，贼新版本是 2014 年 2 月的 V19。在 V19 中，BASIC 轨道现已可用，其中包含基于以下描述的高质量基因定义：“GENCODE Basic 该集旨在提供对大多数用户有用的 GENCODE 转录本注释的简化子集。目标是拥有一个覆盖所有基因座的高质量基本集。选择 GENCODE 注释以包含在基本集中 独立确定每个基因位点的编码和非编码转录本。”
下面是基因解码可以用于变异注释的 GENCODE 基因定义的命令（请注意，如果 humandb/hg19_seq 中没有全基因组 FASTA 文件，基因检测与基因测序机构应该首先执行 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
同样，基因解码可以使用不同的 -dbtype 参数（wgEncodeGencodeCompV19 和 wgEncodeGencodePolyaV19）切换到 GENCODE 的综合注释和 PolyA 注释。
使用这些注释时，务必注意要使用的正确文件名（如果您不确定表名，请使用 UCSC 基因组浏览器中的表浏览器）。
还支持许多其他基因定义系统。 例如，用户可以选择CCDS基因定义。 （请注意，如果 humandb/hg19_seq 中没有全基因组 FASTA 文件，获得基因序列后应该首先执行 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
基因解码技术解释：对于 CCDS 基因，输出将不包含基因名称，而仅包含 CCDS 标识符。 要获取基因名称，基因检测机构必须编写自己的程序来处理 ANNOVAR 输出文件。 有两个表可用于将 CCDS ID 转换为其他 ID：ccdsNotes 将 CCDS 转换为 UCSC 已知基因转录本 ID，然后您可以将其转换为基因名称。 ccdsInfo 表将 CCDS ID 转换为 ENSEMBL 转录本或 RefSeq 转录本，然后您可以进一步将它们转换为基因名称。
对基因测序结果进行解读检测通常会涉及以下几个步骤:
1. 将测序reads对参考基因组进行mapping,得到read alignments。常用的工具包括BWA,Bowtie2等。
2. 根据参考基因组的注释信息(例如GENCODE/CCDS),将read alignments与基因、转录本进行比较,看reads是否可map到已知的基因区域。这可以使用一些visual化浏览器进行,如IGV。
3. 对于未map到已知基因区域的reads,可以进行de novo组装,组装成未知的转录本序列。这可以用一些软件工具完成,如Trinity,SOAPdenovo-Trans等。
4. 将组装得到的转录本与已知蛋白数据库(如UniProt)进行序列比对,判断转录本是否编码未知蛋白。
5. 对coding potential较高的未知转录本,可以进行进一步的功能预测分析,如同源比对判断家族,结构预测等。也可以进行实验验证是否真的表达。
6. 贼终,整合已知基因注释和新发现的转录本信息,完成序列测序分析和检测。可以确定已知基因的表达水平变化,也可以发现编码潜在新蛋白的未知转录本。
综上,利用已有的基因注释数据库(如GENCODE/CCDS)作为参考,结合reads mapping、de novo组装和功能预测等分析,可以较全面地解析和检测基因测序结果。
(责任编辑：广东会GDH基因)
