translationparameters
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SupplementaryTablesAccurateVariantDetectionacrossNon-amplifiedandWholeGenomeAmplifiedDNAUsingTargetedNextGenerationSequencingAbdouElSharawy1,JasonWarner2,JeffOlson2,MichaelForster1,MarkusB.
Schilhabel1,DarrenLink2,StefanRose-John3,StefanSchreiber1,4,PhilipRosenstiel1,JamesBrayer2andAndreFranke1,*1InstituteofClinicalMolecularBiology,Christian-Albrechts-University,Kiel,Germany2RainDanceTechnologies,Inc.
Lexington,Massachusetts,U.
S.
A.
3InstituteofBiochemistry,Christian-Albrechts-University,Kiel,Germany4FirstMedicalClinic,UniversityHospital,Schleswig-Holstein,Kiel,GermanyEmailaddressesAE:a.
sharawy@mucosa.
deJW:WARNERJ@raindancetech.
comJO:OLSONJ@raindancetech.
comMF:m.
forster@ikmb.
uni-kiel.
deMS:m.
schilhabel@ikmb.
uni-kiel.
deDL:dlink@raindancetechnologies.
comSR:rosejohn@biochem.
uni-kiel.
deSS:s.
schreiber@mucosa.
dePR:p.
rosenstiel@mucosa.
deJP:brayerj@raindancetech.
comAF:a.
franke@mucosa.
deSupplementaryTable1:OverviewofSampleProcessing:RainDanceSequenceEnrichment,SOLiDSequencingLibraryConstructionandSampleIndexing,EmulsionPCRandSequencingSampleIDHapMapSample_IDFamilyIDLibraryIDBarCodeEmulsionIDSequencingID1NA12003(gDNA)1420759L1759em759seq2NA12004(gDNA)1420760L2760em760seq3NA10838(gDNA)1420761L3761em761seq4NA11829(gDNA)1350762L4762em762seq5NA11830(gDNA)1350763L5763em763seq6NA10856(gDNA)1350764L6764em764seq1-6_16DNAspooledbeforelibrarypreparation1350and1420768_1L-768_1Lem768_1Lseq1-6_26DNAspooledbeforelibrarypreparation*1350and1420768_2L-768_2Lem768_2Lseq7IndexedSample:pooledbeforeemPCR(pB)1350and1420770L1-4&6770em770seq8Indexedsamples:pooledafteremPCR(pA)1350and1420792L1-6792em792seq9NA12003(WGAgDNA)1420765L9765em765seq10NA12004(WGAgDNA)1420766L10766em766seq11NA10838(WGAgDNA)1420767L11767em767seq*Technicalreplicateoflibrary786_1.
-Boldfaceditalicwordsindicatepooledsamples/libraries.
-gDNA:genomicDNA;WGA:whole-genomeamplification;emPCR:emulsionPCR.
SupplementaryTable2:RainDanceTechnologies384MemberPrimerPanel-gff(AseparateExcelsheet)SupplementaryTable3:CLCBioSNPDetectionParametersAddconflictannotationsNoAlignmentmodelocalAmpliconannotationAnnotateconsensussequenceYesAnnotatereferencesequenceYesColorspacealignmentYesColorspaceAlignmentYesColorspaceerrorcost3ColorspaceErrorCost3ConflictresolutionVoteCreateReportYesCreateSequenceListYesCreatetableYesDeletionCost3GeneticcodetranslationStandardGuidanceonlyNoInsertioncost3InsertionCost3Length0.
5MaskreferencesequenceMatchmoderandomMaxalignments1Maxdistance250Maximumcoverage50000Maximumexpectedvariations(ploidy)2Maximumgapandmismatchcount2Mindistance180Minimumaveragequality15Minimumcentralquality20Minimumcoverage5Minimumpaired-endcoverage0Minimumvariantfrequency(%)10.
0Mismatchcost2MismatchCost2ReadsettingsReferencesequenceschr21,chr22,chrY,chr20,chr19,chr18,chr17,chr16,chr15,chr14,chr13,chr12,chr11,chr10,chr9,chr8,chrX,chr7,chr6,chr5,chr4,chr3,chr2,chr1Reporttype1x,5x,10x,20x,40x,80x,100xScorelimit8SequencemaskingNoSimilarity0.
8UngappedalignmentYesUseannotatedampliconsNoVariantcountthreshold50Windowlength11SupplementaryTable4:CoverageMetricsCLCbioGenomicsWorkbench(version5.
1)HapMapSampleTypeLibraryIDReadsMappedOn-Target%ADoCC1C10C20C30C50C100CoverageSampleID0.
2XMeanNA12003gDNA759L36,453,20819,290,59852.
92%8,577,72244.
47%2309.
4799.
43%98.
47%98.
15%97.
92%97.
39%96.
24%87.
49%WGA765L36,986,94320,508,82555.
45%9,361,66345.
65%2541.
3499.
41%98.
56%98.
15%97.
83%97.
34%96.
54%86.
97%gDNA-pB770L_BC110,031,8095,627,77656.
10%2,489,71044.
24%671.
3298.
82%97.
75%96.
79%96.
16%94.
66%90.
56%87.
63%gDNA-pA792L_BC15,221,8222,678,14851.
29%1,142,28842.
65%302.
7898.
37%96.
43%94.
70%92.
87%89.
08%77.
89%87.
03%NA12004gDNA760L39,005,64619,804,79150.
77%9,852,43249.
75%2606.
7999.
25%98.
37%98.
03%97.
76%97.
37%96.
35%87.
66%WGA766L43,079,25716,264,34437.
75%6,035,72037.
11%1515.
4199.
22%98.
01%97.
45%97.
17%96.
55%94.
84%86.
28%gDNA-pB770L_BC23,272,4241,883,81857.
57%987,46052.
42%266.
7798.
17%96.
45%94.
75%92.
74%88.
77%76.
85%88.
16%gDNA-pA792L_BC26,023,1133,088,31551.
27%1,546,58250.
08%408.
1898.
40%96.
94%95.
64%94.
33%91.
75%84.
79%87.
41%NA10838gDNA761L35,573,70314,695,82341.
31%5,705,05038.
82%1481.
4199.
24%98.
20%97.
73%97.
27%96.
55%94.
89%87.
12%WGA767L43,140,96821,584,86150.
03%8,194,93137.
97%2189.
5999.
42%98.
54%98.
14%97.
80%97.
16%96.
04%87.
69%gDNA-pB770L_BC37,114,6373,869,66254.
39%1,809,01946.
75%489.
7498.
70%97.
19%95.
95%94.
97%92.
83%86.
75%87.
12%gDNA-pA792L_BC36,587,6013,489,97152.
98%1,600,82745.
87%430.
2898.
54%97.
00%95.
71%94.
49%91.
72%85.
08%87.
00%NA11829gDNA762L39,864,62018,798,51647.
16%7,830,28241.
65%2099.
6599.
47%98.
47%98.
09%97.
70%97.
15%96.
00%87.
03%gDNA-pB770L_BC4*638,985354,59955.
49%161,74245.
61%43.
7595.
99%83.
63%66.
47%49.
70%28.
12%9.
87%86.
54%gDNA-pA792L_BC4*677,767335,66649.
53%139,65241.
60%36.
9895.
38%80.
11%59.
39%41.
17%22.
45%6.
88%85.
65%NA11830gDNA763L38,654,83020,144,03352.
11%9,425,15246.
79%2557.
1799.
53%98.
61%98.
21%97.
92%97.
42%96.
45%87.
07%gDNA-pB770L_BC5InsufficientamountofmaterialtorunsamplegDNA-pA792L_BC55,403,5602,832,41152.
42%1,296,85045.
79%346.
1998.
38%96.
87%95.
24%93.
64%90.
28%81.
46%86.
91%NA10856gDNA764L43,185,70722,650,13752.
45%9,489,38241.
90%2574.
9499.
53%98.
68%98.
24%98.
01%97.
58%96.
55%86.
90%gDNA-pB770L_BC69,255,3335,136,66455.
50%2,156,02041.
97%584.
6398.
90%97.
62%96.
70%95.
74%93.
93%89.
00%87.
30%gDNA-pA792L_BC66,435,6903,407,87552.
95%1,423,55441.
77%381.
0398.
64%96.
96%95.
54%93.
84%90.
87%82.
48%86.
57%PooledSamplesgDNA768L_141,913,86021,748,40251.
89%9,833,00745.
21%2627.
2799.
55%98.
63%98.
22%98.
05%97.
67%96.
85%87.
01%gDNA768L_241,958,62822,079,02252.
62%10,073,99545.
63%2700.
4499.
47%98.
66%98.
25%98.
08%97.
69%96.
90%87.
25%SupplementaryTable5:AnoverviewofallSNPsandgenotypesdetected(AseparateExcelsheet)SupplementaryTable6:SequenceDataGeneratedusing454FLXandIlluminaoftheSameTargetRegions(172kb/384exons)TargetedSequencingResults454FLXIlluminaTotalReads219,8765,954,822ReadsMappingtoTargetRegions184,6412,337,390AverageMappedReadsperAmplicon4825,343PercentofTargetAmpliconsCovered99.
7%99.
7%TargetUniformity(<10-fold)96%98%SupplementaryTable7:SampleMultiplexingCalculationLibraryIDBar-codeReadsMappedtoGenomeMappedonTarget792LBC15,221,82231.
60%64.
20%BC26,023,11332.
50%72.
90%BC36,587,60134.
00%67.
60%BC4677,76728.
50%66.
40%BC55,403,56032.
80%68.
10%BC69,255,33336.
30%61.
30%TotalReads(BC1-BC6)33,169,196Average(BC1-BC6)32.
62%66.
75%TotalReadsperOctetA33,169,196Average%ofReadsMappedtoGenomeB32.
62%MappedReadsC10,818,686=A*B%ofreadonTargetD66.
75%ReadsonTargetE7,221,473=C*DReadlength(bases)F50BasesperOctetG361,073,648=E*FBasesperSample*H17,280,500SamplesperOctetI20=G/HSampleperFlowCellJ160=I*8SamplesperRunK320=I*16*BasesperSample=#ofampliconbases*100
Schilhabel1,DarrenLink2,StefanRose-John3,StefanSchreiber1,4,PhilipRosenstiel1,JamesBrayer2andAndreFranke1,*1InstituteofClinicalMolecularBiology,Christian-Albrechts-University,Kiel,Germany2RainDanceTechnologies,Inc.
Lexington,Massachusetts,U.
S.
A.
3InstituteofBiochemistry,Christian-Albrechts-University,Kiel,Germany4FirstMedicalClinic,UniversityHospital,Schleswig-Holstein,Kiel,GermanyEmailaddressesAE:a.
sharawy@mucosa.
deJW:WARNERJ@raindancetech.
comJO:OLSONJ@raindancetech.
comMF:m.
forster@ikmb.
uni-kiel.
deMS:m.
schilhabel@ikmb.
uni-kiel.
deDL:dlink@raindancetechnologies.
comSR:rosejohn@biochem.
uni-kiel.
deSS:s.
schreiber@mucosa.
dePR:p.
rosenstiel@mucosa.
deJP:brayerj@raindancetech.
comAF:a.
franke@mucosa.
deSupplementaryTable1:OverviewofSampleProcessing:RainDanceSequenceEnrichment,SOLiDSequencingLibraryConstructionandSampleIndexing,EmulsionPCRandSequencingSampleIDHapMapSample_IDFamilyIDLibraryIDBarCodeEmulsionIDSequencingID1NA12003(gDNA)1420759L1759em759seq2NA12004(gDNA)1420760L2760em760seq3NA10838(gDNA)1420761L3761em761seq4NA11829(gDNA)1350762L4762em762seq5NA11830(gDNA)1350763L5763em763seq6NA10856(gDNA)1350764L6764em764seq1-6_16DNAspooledbeforelibrarypreparation1350and1420768_1L-768_1Lem768_1Lseq1-6_26DNAspooledbeforelibrarypreparation*1350and1420768_2L-768_2Lem768_2Lseq7IndexedSample:pooledbeforeemPCR(pB)1350and1420770L1-4&6770em770seq8Indexedsamples:pooledafteremPCR(pA)1350and1420792L1-6792em792seq9NA12003(WGAgDNA)1420765L9765em765seq10NA12004(WGAgDNA)1420766L10766em766seq11NA10838(WGAgDNA)1420767L11767em767seq*Technicalreplicateoflibrary786_1.
-Boldfaceditalicwordsindicatepooledsamples/libraries.
-gDNA:genomicDNA;WGA:whole-genomeamplification;emPCR:emulsionPCR.
SupplementaryTable2:RainDanceTechnologies384MemberPrimerPanel-gff(AseparateExcelsheet)SupplementaryTable3:CLCBioSNPDetectionParametersAddconflictannotationsNoAlignmentmodelocalAmpliconannotationAnnotateconsensussequenceYesAnnotatereferencesequenceYesColorspacealignmentYesColorspaceAlignmentYesColorspaceerrorcost3ColorspaceErrorCost3ConflictresolutionVoteCreateReportYesCreateSequenceListYesCreatetableYesDeletionCost3GeneticcodetranslationStandardGuidanceonlyNoInsertioncost3InsertionCost3Length0.
5MaskreferencesequenceMatchmoderandomMaxalignments1Maxdistance250Maximumcoverage50000Maximumexpectedvariations(ploidy)2Maximumgapandmismatchcount2Mindistance180Minimumaveragequality15Minimumcentralquality20Minimumcoverage5Minimumpaired-endcoverage0Minimumvariantfrequency(%)10.
0Mismatchcost2MismatchCost2ReadsettingsReferencesequenceschr21,chr22,chrY,chr20,chr19,chr18,chr17,chr16,chr15,chr14,chr13,chr12,chr11,chr10,chr9,chr8,chrX,chr7,chr6,chr5,chr4,chr3,chr2,chr1Reporttype1x,5x,10x,20x,40x,80x,100xScorelimit8SequencemaskingNoSimilarity0.
8UngappedalignmentYesUseannotatedampliconsNoVariantcountthreshold50Windowlength11SupplementaryTable4:CoverageMetricsCLCbioGenomicsWorkbench(version5.
1)HapMapSampleTypeLibraryIDReadsMappedOn-Target%ADoCC1C10C20C30C50C100CoverageSampleID0.
2XMeanNA12003gDNA759L36,453,20819,290,59852.
92%8,577,72244.
47%2309.
4799.
43%98.
47%98.
15%97.
92%97.
39%96.
24%87.
49%WGA765L36,986,94320,508,82555.
45%9,361,66345.
65%2541.
3499.
41%98.
56%98.
15%97.
83%97.
34%96.
54%86.
97%gDNA-pB770L_BC110,031,8095,627,77656.
10%2,489,71044.
24%671.
3298.
82%97.
75%96.
79%96.
16%94.
66%90.
56%87.
63%gDNA-pA792L_BC15,221,8222,678,14851.
29%1,142,28842.
65%302.
7898.
37%96.
43%94.
70%92.
87%89.
08%77.
89%87.
03%NA12004gDNA760L39,005,64619,804,79150.
77%9,852,43249.
75%2606.
7999.
25%98.
37%98.
03%97.
76%97.
37%96.
35%87.
66%WGA766L43,079,25716,264,34437.
75%6,035,72037.
11%1515.
4199.
22%98.
01%97.
45%97.
17%96.
55%94.
84%86.
28%gDNA-pB770L_BC23,272,4241,883,81857.
57%987,46052.
42%266.
7798.
17%96.
45%94.
75%92.
74%88.
77%76.
85%88.
16%gDNA-pA792L_BC26,023,1133,088,31551.
27%1,546,58250.
08%408.
1898.
40%96.
94%95.
64%94.
33%91.
75%84.
79%87.
41%NA10838gDNA761L35,573,70314,695,82341.
31%5,705,05038.
82%1481.
4199.
24%98.
20%97.
73%97.
27%96.
55%94.
89%87.
12%WGA767L43,140,96821,584,86150.
03%8,194,93137.
97%2189.
5999.
42%98.
54%98.
14%97.
80%97.
16%96.
04%87.
69%gDNA-pB770L_BC37,114,6373,869,66254.
39%1,809,01946.
75%489.
7498.
70%97.
19%95.
95%94.
97%92.
83%86.
75%87.
12%gDNA-pA792L_BC36,587,6013,489,97152.
98%1,600,82745.
87%430.
2898.
54%97.
00%95.
71%94.
49%91.
72%85.
08%87.
00%NA11829gDNA762L39,864,62018,798,51647.
16%7,830,28241.
65%2099.
6599.
47%98.
47%98.
09%97.
70%97.
15%96.
00%87.
03%gDNA-pB770L_BC4*638,985354,59955.
49%161,74245.
61%43.
7595.
99%83.
63%66.
47%49.
70%28.
12%9.
87%86.
54%gDNA-pA792L_BC4*677,767335,66649.
53%139,65241.
60%36.
9895.
38%80.
11%59.
39%41.
17%22.
45%6.
88%85.
65%NA11830gDNA763L38,654,83020,144,03352.
11%9,425,15246.
79%2557.
1799.
53%98.
61%98.
21%97.
92%97.
42%96.
45%87.
07%gDNA-pB770L_BC5InsufficientamountofmaterialtorunsamplegDNA-pA792L_BC55,403,5602,832,41152.
42%1,296,85045.
79%346.
1998.
38%96.
87%95.
24%93.
64%90.
28%81.
46%86.
91%NA10856gDNA764L43,185,70722,650,13752.
45%9,489,38241.
90%2574.
9499.
53%98.
68%98.
24%98.
01%97.
58%96.
55%86.
90%gDNA-pB770L_BC69,255,3335,136,66455.
50%2,156,02041.
97%584.
6398.
90%97.
62%96.
70%95.
74%93.
93%89.
00%87.
30%gDNA-pA792L_BC66,435,6903,407,87552.
95%1,423,55441.
77%381.
0398.
64%96.
96%95.
54%93.
84%90.
87%82.
48%86.
57%PooledSamplesgDNA768L_141,913,86021,748,40251.
89%9,833,00745.
21%2627.
2799.
55%98.
63%98.
22%98.
05%97.
67%96.
85%87.
01%gDNA768L_241,958,62822,079,02252.
62%10,073,99545.
63%2700.
4499.
47%98.
66%98.
25%98.
08%97.
69%96.
90%87.
25%SupplementaryTable5:AnoverviewofallSNPsandgenotypesdetected(AseparateExcelsheet)SupplementaryTable6:SequenceDataGeneratedusing454FLXandIlluminaoftheSameTargetRegions(172kb/384exons)TargetedSequencingResults454FLXIlluminaTotalReads219,8765,954,822ReadsMappingtoTargetRegions184,6412,337,390AverageMappedReadsperAmplicon4825,343PercentofTargetAmpliconsCovered99.
7%99.
7%TargetUniformity(<10-fold)96%98%SupplementaryTable7:SampleMultiplexingCalculationLibraryIDBar-codeReadsMappedtoGenomeMappedonTarget792LBC15,221,82231.
60%64.
20%BC26,023,11332.
50%72.
90%BC36,587,60134.
00%67.
60%BC4677,76728.
50%66.
40%BC55,403,56032.
80%68.
10%BC69,255,33336.
30%61.
30%TotalReads(BC1-BC6)33,169,196Average(BC1-BC6)32.
62%66.
75%TotalReadsperOctetA33,169,196Average%ofReadsMappedtoGenomeB32.
62%MappedReadsC10,818,686=A*B%ofreadonTargetD66.
75%ReadsonTargetE7,221,473=C*DReadlength(bases)F50BasesperOctetG361,073,648=E*FBasesperSample*H17,280,500SamplesperOctetI20=G/HSampleperFlowCellJ160=I*8SamplesperRunK320=I*16*BasesperSample=#ofampliconbases*100
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