List of flagged samples run 1

Author: Peter-Bram 't Hoen
Date: 5-February-2014

There are three fields in the metadatabase to flag samples that should not be used in the final analysis: QC of the sequencing, genotype concordance and contamination. Here we report the final list of samples which are flagged in the metadatabase.

QC flag

These three samples are flagged because of too low number of reads:
Too few reads:
AC1JV9ACXX-1-10
AD1NE2ACXX-5-22
BD1NW4ACXX-3-27

Other reasons: See ​http://www.bbmriwiki.nl/wiki/FgQualityControl/FgQualityControlRun1
BD1NYRACXX-6-10 too low percentage of mapped reads, outlier on principal component 1,4,5,6
AD2CJPACXX-8-9 low exon correlation, outlier on principal component 1,11,14
BD1NR9ACXX-7-27 low percentage of mapped reads, outlier on principal component 4, likely degraded

Genotype concordance

This is the list of the samples from the different cohorts that have a mismatch between RNA and DNA genotypes that could not be corrected since there is no additional lab evidence suggesting a sample swap. For more information, see ​http://www.bbmriwiki.nl/wiki/FgSampleBlacklist
CODAM:
AD10W1ACXX-5-18
AD10W1ACXX-8-11
LL:
AC1C40ACXX-4-4
AD1GWFACXX-4-15
RS:
AD1NNNACXX-4-18
AC1JV9ACXX-1-13
BC1JTJACXX-6-7
BC1KAVACXX-8-13
LLS:
BD1NW4ACXX-7-13
BD1NYRACXX-2-27
BC1KBKACXX-5-8
AD1NAMACXX-7-19
BC1KBKACXX-5-6
AD2DATACXX-8-1
BD2D5MACXX-4-15
BD2D5MACXX-3-7
AD2DATACXX-3-21
AD2DATACXX-4-5
AD1NFNACXX-8-25
BD24PGACXX-7-8
BD2CPRACXX-1-12
AD2DATACXX-3-22
BD24PGACXX-7-10
BD2CPRACXX-1-21
BC1KBKACXX-5-3
AD1NFNACXX-8-27
BD24PGACXX-8-25
BC1KBKACXX-5-7
BD24PGACXX-6-12
BD1NW4ACXX-8-5
BC1KBKACXX-3-12
BC1KBKACXX-5-1
AD2CJPACXX-6-9
BD1NYRACXX-2-16
AD2CJPACXX-5-1
AD1NE2ACXX-4-22
BC1KBKACXX-5-2
BC1KBKACXX-5-5
BD1NYRACXX-3-1
BD2D5MACXX-2-25
BD1NYRACXX-4-19
AD1NFNACXX-4-8
BD1NYRACXX-2-15
BC1KBKACXX-5-4
AD1NFNACXX-5-15

Contaminations

No contaminations have been detected for CODAM, RS, LL. Only outlier samles in heterozygosity rates have already been spotted as mixups. See: ​http://www.bbmriwiki.nl/wiki/FgSampleBlacklist
The list of LLS samples that have high heterozygosity rate based on genotypes called from RNAseq data (all of them have low genotype concordance - see the list above):
BD1NYRACXX-2-27
BC1KBKACXX-5-8
BC1KBKACXX-5-6
BD24PGACXX-7-10
BC1KBKACXX-5-3
BC1KBKACXX-5-7
BD1NW4ACXX-8-5
BC1KBKACXX-5-1
BD1NYRACXX-2-16
AD1NE2ACXX-4-22
BC1KBKACXX-5-2
BC1KBKACXX-5-5
BD1NYRACXX-3-1
BD1NYRACXX-4-19
AD1NFNACXX-4-8
BC1KBKACXX-5-4
AD1NFNACXX-5-15

Overview RNAseq data April 14th 2014

Table I: Overview of the RNAseq data.

Biobank	Person Id	RNAseq run Id	Data part of RP31	Passed QC
CODAM	192	191	191	188
LL	761	630	630	628
LLS	821	720	697(23)2	664
NTR	3300	-	-	-
RS	768	658	658	652
Total:	5842	2199	2176	2132

¹All these samples are also part of the data freeze 1. ²23 samples are not part of RP3.

There are 29 merged runs in the passed qc rnaseq data: 2 for CODAM, 17 for LL, 4 for LLS and 6 for RS.

Table II: Detail of samples that did not passed quality control.

Biobank	Not Passed QC	Bad quality	Genotype Discordance	Contaminated
CODAM	3	1	2	-
LL	2	-	2	-
LLS	341	3	322	17
RS	6	2	4	-
Total:	45	6	40	17

1One sample not part of RP3. ²Three LLS swaps identified by MixupMapper have been corrected. Additional evidence confirmed that these LLS samples were indeed swapped. These six samples are not included in the Genotype Discordance counts for LLS.

Table III: Overview genotype data (GoNL version 5 imputed)

Biobank	Person Id	Genotype1	Overlapping with Passed QC RNAseq data
CODAM	192	188 (4)2	184 (4)3
LL	761	756 (5)	626 (2)4
LLS	821	765 (56)	654 (10)5
NTR	3300	1886 (1414)	-
RS	768	768	652
Total:	5842	4363 (1479)	2116 (16)

¹Genotype information was extracted from the biobank genotype sample information files GoNL version 5 imputed data, directly extracted from the SRM. ²Numbers between brackets indicated the differences between number of person ids and genotype data available. ³Missing genotypes for: CODAM-2037, CODAM-2074, CODAM-2175 and CODAM-2555. ⁴Missing genotypes for: LL-LLDeep_0127 and LL-LLDeep_0519. ⁵These 10 samples are GoNL samples for which no genotype data was provided.

LLS update

For LLS the detected sample swaps were swapped back. The mixup mapper and genotype concordance check performed using the final sample sheets show no mixups and no strong outliers.