RBC membrane disorders NGS panel
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The RBC Membrane AmpliSeq Panel v1 (IAD89957_197) is covering 99.05% of the desired regions (all coding regions (exons), flanking intronic regions, untranslated regions and promotor areas with known (likely) pathogenic variants).: SPTA1, SPTB, ANK1, SLC4A1, EPB41, EPB42, RHAG, PIEZO1, SEC23B and UGT1A1 and include all known disease making variants listed in HGMD professional (Version HGMD 2015.3) (see Table 1 and 2)
Table 1: List of submitted genes and coverage of the design
Gene |
Chromo-some |
NCBI Transcript |
Exons |
Submitted Bases |
Coverage |
Coverage 5' of initiation site (flanking sequence and 5'UTR) |
Ampli-cons |
ANK1 |
chr8 |
NM_001142446.1 |
43 |
3026 |
100,00% |
204 base before initiation site |
57 |
EPB41 |
chr1 |
NM_001166005.1 |
21 |
2806 |
100,00% |
149 base before initiation site |
20 |
EPB42 |
chr15 |
NM_000119.2 |
13 |
2296 |
100,00% |
68 base before initiation site |
15 |
PIEZO1 |
chr16 |
NM_001142864.2 |
51 |
8076 |
99,42% |
base 34 of exon1 |
62 |
UGT1A1 |
chr2 |
NM_000463.2 |
5 |
1892 |
100,00% |
124 base before initiation site |
10 |
RHAG |
chr6 |
NM_000324.2 |
10 |
1330 |
100,00% |
95 base before initiation site |
10 |
SEC23B |
chr20 |
NM_032986.3 |
20 |
3455 |
100,00% |
46 base before initiation site |
28 |
SLC4A1 |
chr17 |
NM_000342.3 |
20 |
2926 |
100,00% |
83 base before initiation site + regions of -3420 and -2865 before init. site |
23 |
SPTA1 |
chr1 |
NM_003126.2 |
52 |
7780 |
96,85% |
154 base before exon 2 |
52 |
SPTB |
chr14 |
NM_001024858.2 |
35 |
7406 |
100,00% |
240 base before exon 1 (incl promotor) |
50 |
Table 2: List of missed bases in design
Genes |
Coverage |
Number Missing Bases |
GRCh37/hg19 coordinates |
Description |
Missing HGMD-DM variants |
ANK1 |
99,42% |
38 |
chr8:41753965-41754003 |
flanking region and first 33 bases exon 1 |
non |
PIEZO1 |
96,85% |
74 |
chr16:88851303-88851377 |
both flanking regios and Exon 1 (64 bases) |
non |
|
|
|
17 |
chr16:88803041-88803058 |
flanking region and last 12 bases exon 11 |
non |
|
|
|
5 |
chr16:88800153-88800158 |
flanking site (5base) of 5' exon 18 |
non |
|
|
|
158 |
chr16:88782374-88782532 |
flanking region and first 153 bases exon 50 |
non |
The percentage of target bases that is covered at least 20 times (%Base20x) is at least 99.44% for the recommended Mapped Reads of 750.000. This acceptance criteria will result in a coverage of all published disease causing variants listed in HGMD (downloaded November 2015). Two partial exon regions and their flanking intronic regions are not covered for 20 times. Both regions do not contain disease causing variants listed in HGMD professional (Version HGMD 2015.3).
Table 3: Bases possibly missed in exons and flanking intronic regions
Chr |
GRCh37/hg19 coordinates |
Amplicon id |
Gene |
Missing Bases |
Exon |
Missing HGMD |
|
|
|
Start |
End |
|
|
|
|
|
chr16 |
88798299 |
88798318 |
AMPL7155929112 |
PIEZO1 |
20 |
22 |
non |
chr16 |
88786834 |
88786940 |
AMPL7155930944 |
PIEZO1 |
106 |
12 |
non |
Read more about technique and reporting in the background information.
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