怎样进行高密度(HD)查找

在CGH高密度探针查找中，哪个相似度筛选器能够符合我的设计要求？使用或不使用筛选器的后果是什么？

当选中“无筛选器”时，任何探针都可能被选择，无论与其他的基因组位点有多大的相似度。请记住，“非唯一”探针的数据将更加难以解释，使用“非唯一探针筛选器”选项来限制最大完美基因组击中数就会很有帮助。

当选中“完美匹配筛选器”时（或在“非唯一探针筛选器”完美的基因组命中的最大数量设置为1），含有一个以上的完美匹配基因的探针被排除在外，并将因此无法在Segmental Duplication或Pseudo-Autosomal Regions (PAR)中找到复制探针。“相似度评分”筛选器是最严格的筛选器。

该筛选器排除了与基因组其他位点有显著相似度的探针，并且将有无法找到探针的基因组区域。

 

In the CGH HD Probe Search, how do I target exons only, not just genes?

• Using the Include Regions and selecting Exonic will limit the probes returned to those marked as overlapping exons only. This will work when searching by genomic intervals or gene annotations (transcript and gene identifiers). The designer should be aware that exons typically are more GC-rich than the rest of the genome, these probes, in general, will have a lower probe scores. See the FAQ ”What is a CGH probe score?” for more information. Using this “Exonic” approach there is no possibility to select the nearest probes in introns instead.

• Identify the coordinates for the exons outside of eArray and use them as Genomic Intervals to select probes in. Then with the “Extended Interval Boundary” option in eArray the Genomic Intervals can be extended beyond the exon boundaries with a selected number of base pairs. Here are the instructions on how to identify coordinates for exons in UCSC.

Using the Table Browser utility from the UCSC genome browser, make sure the proper species and genome build are selected from the drop-down lists. It is important that the build matches eArray. For “track”, select desired gene definition track, Agilent recommends “CCDS”, “RefSeq Genes”, or “UCSC genes”. Follow the UCSC instructions on how to restrict the search. Options include filtering on genomic regions or track identifiers (names/accessions). Make sure the output contains chrom, exonStarts and exonEnds. This will give you all of the exon coordinates for the regions you defined.

To input these locations into an eArray HD Probe Search, split the line into pieces (one for each exon) and adjust the start coordinate (the output is 0-based, eArray expects 1-based). The orientation (i.e., strand information) does not matter in an eArray probe search. For example, the following line defining three exons (chrom; exon count; exon starts; exon ends):

chr1; 3; 2450045, 2451144, 2451409; 2451048, 2451310, 2451544

Can be converted to the format needed in eArray.:

chr1:2450046-2451048
chr1:2451145-2451310
chr1:2451410-2451544

 

 

In the CGH HD Probe Search, how do I target exons only, not just genes?

• Using the Include Regions and selecting Exonic will limit the probes returned to those marked as overlapping exons only. This will work when searching by genomic intervals or gene annotations (transcript and gene identifiers). The designer should be aware that exons typically are more GC-rich than the rest of the genome, these probes, in general, will have a lower probe scores. See the FAQ ”What is a CGH probe score?” for more information. Using this “Exonic” approach there is no possibility to select the nearest probes in introns instead.

• Identify the coordinates for the exons outside of eArray and use them as Genomic Intervals to select probes in. Then with the “Extended Interval Boundary” option in eArray the Genomic Intervals can be extended beyond the exon boundaries with a selected number of base pairs. Here are the instructions on how to identify coordinates for exons in UCSC.

Using the Table Browser utility from the UCSC genome browser, make sure the proper species and genome build are selected from the drop-down lists. It is important that the build matches eArray. For “track”, select desired gene definition track, Agilent recommends “CCDS”, “RefSeq Genes”, or “UCSC genes”. Follow the UCSC instructions on how to restrict the search. Options include filtering on genomic regions or track identifiers (names/accessions). Make sure the output contains chrom, exonStarts and exonEnds. This will give you all of the exon coordinates for the regions you defined.

To input these locations into an eArray HD Probe Search, split the line into pieces (one for each exon) and adjust the start coordinate (the output is 0-based, eArray expects 1-based). The orientation (i.e., strand information) does not matter in an eArray probe search. For example, the following line defining three exons (chrom; exon count; exon starts; exon ends):

chr1; 3; 2450045, 2451144, 2451409; 2451048, 2451310, 2451544

Can be converted to the format needed in eArray.:

chr1:2450046-2451048
chr1:2451145-2451310
chr1:2451410-2451544

 

 

在CGH高密度探针查找中，哪个相似度筛选器能够符合我的设计要求？使用或不使用筛选器的后果是什么？

当选中“无筛选器”时，任何探针都可能被选择，无论与其他的基因组位点有多大的相似度。请记住，“非唯一”探针的数据将更加难以解释，使用“非唯一探针筛选器”选项来限制最大完美基因组击中数就会很有帮助。

当选中“完美匹配筛选器”时（或在“非唯一探针筛选器”完美的基因组命中的最大数量设置为1），含有一个以上的完美匹配基因的探针被排除在外，并将因此无法在Segmental Duplication或Pseudo-Autosomal Regions (PAR)中找到复制探针。“相似度评分”筛选器是最严格的筛选器。

该筛选器排除了与基因组其他位点有显著相似度的探针，并且将有无法找到探针的基因组区域。

 

In the CGH HD Probe Search, how do I target exons only, not just genes?

• Using the Include Regions and selecting Exonic will limit the probes returned to those marked as overlapping exons only. This will work when searching by genomic intervals or gene annotations (transcript and gene identifiers). The designer should be aware that exons typically are more GC-rich than the rest of the genome, these probes, in general, will have a lower probe scores. See the FAQ ”What is a CGH probe score?” for more information. Using this “Exonic” approach there is no possibility to select the nearest probes in introns instead.

• Identify the coordinates for the exons outside of eArray and use them as Genomic Intervals to select probes in. Then with the “Extended Interval Boundary” option in eArray the Genomic Intervals can be extended beyond the exon boundaries with a selected number of base pairs. Here are the instructions on how to identify coordinates for exons in UCSC.

Using the Table Browser utility from the UCSC genome browser, make sure the proper species and genome build are selected from the drop-down lists. It is important that the build matches eArray. For “track”, select desired gene definition track, Agilent recommends “CCDS”, “RefSeq Genes”, or “UCSC genes”. Follow the UCSC instructions on how to restrict the search. Options include filtering on genomic regions or track identifiers (names/accessions). Make sure the output contains chrom, exonStarts and exonEnds. This will give you all of the exon coordinates for the regions you defined.

To input these locations into an eArray HD Probe Search, split the line into pieces (one for each exon) and adjust the start coordinate (the output is 0-based, eArray expects 1-based). The orientation (i.e., strand information) does not matter in an eArray probe search. For example, the following line defining three exons (chrom; exon count; exon starts; exon ends):

chr1; 3; 2450045, 2451144, 2451409; 2451048, 2451310, 2451544

Can be converted to the format needed in eArray.:

chr1:2450046-2451048
chr1:2451145-2451310
chr1:2451410-2451544