@HD VN:1.4 SO:coordinate @RG ID:22039_8#5 PL:ILLUMINA PU:170306_HS32_22039_A_CAJWAANXX_8#5 LB:18594598 DS:EGAS00001002273: Gastric neuroendocrine tumors (gNETs) occur with an estimated frequency of 2 per 100,000 in the general population. Type I gastric neuroendocrine tumors (NETs) represent the 75% of gNTEs and arise from gastric enterochromaffin-like (ECL) cells. They have late age of onset and usually benigh course. Classically, hypergastrinemia in patients who have autoimmune atrophic gastritis, causes hyperplasia of gastric ECL cells that progresses into type I gastric NETs and parietal cell (PC) destruction. The genetic bases in families with this disease are unknown. We performed an exome sequencing study of an atypical aggressive familial gNETs case (with early age onset, nodal infiltrations and gastric adenocarcinomas) that followed a recessive model. We identified a deleterious mutation in homozygosis in the ATP4A gene, which encodes the proton pump responsible for acid secretion by gastric parietal cells. This mutation lead to achlorhydria first, and hypergastrinemia and gNET developing as consequence (Calvete et al. 2014). Recently, two more families with gNETs, classical clinical traits and recessive model have been studies by WES but we didn't find any mutation in the ATP4a gene. However, putative mutations affecting genes that contribute to the development and the integrity of PC have been found suggesting that genetic alterations associated to this disorder target to a unique cell type (parietal cells). In order to cinfirm this hypothesis, it is necessary the search for new genes implicated in the gNETs, more familial cases are needed to be studied. We have identified four more new familial gNETs cases. Here, we propose their study by WES. The first family is formed by thress siblings with gNETs. The other families include two siblings with gNETs. This data is part of a pre-publication release. For information on the proper use of pre-publication data shared by the Wellcome Trust Sanger Institute (including details of any publication moratoria), please see http://www.sanger.ac.uk/datasharing/ DT:2017-03-06T00:00:00+0000 PG:SCS SM:EGAN00001487502 CN:SC @PG ID:SCS PN:RTA VN:1.18.66.3 DS:Controlling software on instrument @PG ID:basecalling PN:RTA PP:SCS VN:1.18.66.3 DS:Basecalling Package @PG ID:bambi PN:bambi PP:basecalling VN:0.9.4 DS:Convert Illumina BCL to BAM or SAM file CL:/software/solexa/pkg/bambi/0.9.4/bin/bambi i2b --intensity-dir=/nfs/sf46/ILorHSany_sf46/analysis/170306_HS32_22039_A_CAJWAANXX/Data/Intensities --basecalls-dir=/nfs/sf46/ILorHSany_sf46/analysis/170306_HS32_22039_A_CAJWAANXX/Data/Intensities/BaseCalls --lane=8 --platform-unit=170306_HS32_22039_A_CAJWAANXX_8 --read-group-id=22039_8 --study-name="EGAS00001002273: Gastric neuroendocrine tumors (gNETs) occur with an estimated frequency of 2 per 100,000 in the general population. Type I gastric neuroendocrine tumors (NETs) represent the 75% of gNTEs and arise from gastric enterochromaffin-like (ECL) cells. They have late age of onset and usually benigh course. Classically, hypergastrinemia in patients who have autoimmune atrophic gastritis, causes hyperplasia of gastric ECL cells that progresses into type I gastric NETs and parietal cell (PC) destruction. The genetic bases in families with this disease are unknown. We performed an exome sequencing study of an atypical aggressive familial gNETs case (with early age onset, nodal infiltrations and gastric adenocarcinomas) that followed a recessive model. We identified a deleterious mutation in homozygosis in the ATP4A gene, which encodes the proton pump responsible for acid secretion by gastric parietal cells. This mutation lead to achlorhydria first, and hypergastrinemia and gNET developing as consequence (Calvete et al. 2014). Recently, two more families with gNETs, classical clinical traits and recessive model have been studies by WES but we didn't find any mutation in the ATP4a gene. However, putative mutations affecting genes that contribute to the development and the integrity of PC have been found suggesting that genetic alterations associated to this disorder target to a unique cell type (parietal cells). In order to cinfirm this hypothesis, it is necessary the search for new genes implicated in the gNETs, more familial cases are needed to be studied. We have identified four more new familial gNETs cases. Here, we propose their study by WES. The first family is formed by thress siblings with gNETs. The other families include two siblings with gNETs. This data is part of a pre-publication release. For information on the proper use of pre-publication data shared by the Wellcome Trust Sanger Institute (including details of any publication moratoria), please see http://www.sanger.ac.uk/datasharing/" --sample-alias=EGAN00001487496,EGAN00001487497,EGAN00001487498,EGAN00001487499,EGAN00001487502,EGAN00001487503,EGAN00001487504 --output-file=- --compression-level=0 @PG ID:bamadapterfind PN:bamadapterfind PP:bambi VN:2.0.65 CL:/software/solexa/pkg/biobambam/2.0.65/bin/bamadapterfind level=0 @PG ID:bambi.1 PN:bambi PP:bamadapterfind VN:0.9.4 CL:/software/solexa/pkg/bambi/0.9.4/bin/bambi decode --metrics-file /nfs/sf46/ILorHSany_sf46/analysis/170306_HS32_22039_A_CAJWAANXX/Data/Intensities/BAM_basecalls_20170308-235743/22039_8.bam.tag_decode.metrics --barcode-file /nfs/sf46/ILorHSany_sf46/analysis/170306_HS32_22039_A_CAJWAANXX/Data/Intensities/BAM_basecalls_20170308-235743/metadata_cache_22039/lane_8.taglist --compression-level 0 - @PG ID:bamcollate2 PN:bamcollate2 PP:bambi.1 VN:2.0.65 CL:/software/solexa/pkg/biobambam/2.0.65/bin/bamcollate2 collate=2 level=0 @PG ID:bwa PN:bwa PP:bamcollate2 VN:0.7.15-r1140 CL:/software/solexa/pkg/bwa/0.7.15/bwa sampe /lustre/scratch117/core/sciops_repository/references/PhiX/Sanger-SNPs/all/bwa0_6/phix_unsnipped_short_no_N.fa /tmp/33Mxeax2pD/alnphix_bwa_aln_1_out /tmp/YluyRUSx4J/alnphix_bwa_aln_2_out /tmp/biv2GPMUeZ/alnphix_simple_cat1_out /tmp/USALi1XyQs/alnphix_simple_cat2_out @PG ID:scramble PN:scramble PP:bwa VN:1.14.8 CL:/software/solexa/pkg/scramble/1.14.8/bin/scramble -0 -t 2 -I sam -O bam @PG ID:bam12auxmerge PN:bam12auxmerge PP:scramble VN:2.0.65 CL:/software/solexa/pkg/biobambam/2.0.65/bin/bam12auxmerge level=0 rankstrip=1 ranksplit=1 zztoname=0 clipreinsert=1 /tmp/iLS68YB5Zt/simple_cat_out @PG ID:scramble.1 PN:scramble PP:bam12auxmerge VN:1.14.8 CL:/software/solexa/pkg/scramble/1.14.8/bin/scramble -I bam -O cram -x -3 @PG ID:scramble.2 PN:scramble PP:scramble.1 VN:1.14.8 CL:/software/solexa/pkg/scramble/1.14.8/bin/scramble -I cram -O bam -0 @PG ID:spf PN:spatial_filter PP:scramble.2 DS:A program to apply a spatial filter VN:v10.27-dirty CL:/software/solexa/pkg/pb_calibration/10.27/bin/spatial_filter -c -F /dev/stdout -t /nfs/sf46/ILorHSany_sf46/analysis/170306_HS32_22039_A_CAJWAANXX/Data/Intensities/BAM_basecalls_20170308-235743/no_cal/archive/qc/tileviz/22039_8 --region_size 200 --region_mismatch_threshold 0.0160 --region_insertion_threshold 0.0160 --region_deletion_threshold 0.0160 /dev/stdin ; /software/solexa/pkg/pb_calibration/10.27/bin/spatial_filter -a -f -u -l /nfs/sf46/ILorHSany_sf46/analysis/170306_HS32_22039_A_CAJWAANXX/Data/Intensities/BAM_basecalls_20170308-235743/no_cal/22039_8.bam.filter.stats -F /tmp/YIxQjxmrno/tee_post_filter_creation:__APPLY_FILTER_OUT___out /dev/stdin @PG ID:samtools PN:samtools PP:spf VN:1.3.1-npg-Sep2016 CL:/software/solexa/pkg/samtools/1.3.1-npg-Dec2016/bin/samtools split -f /nfs/sf46/ILorHSany_sf46/analysis/170306_HS32_22039_A_CAJWAANXX/Data/Intensities/BAM_basecalls_20170308-235743/no_cal/lane8/%!.bam - @PG ID:bamcollate2' PN:bamcollate2 PP:samtools VN:2.0.65 CL:/software/solexa/pkg/biobambam/2.0.65/bin/bamcollate2 collate=1 level=0 @PG ID:bamreset PN:bamreset PP:bamcollate2' VN:2.0.65 CL:/software/solexa/pkg/biobambam/2.0.65/bin/bamreset resetaux=0 level=0 verbose=0 @PG ID:bamadapterclip PN:bamadapterclip PP:bamreset VN:2.0.65 CL:/software/solexa/pkg/biobambam/2.0.65/bin/bamadapterclip verbose=0 level=0 @PG ID:bwa' PN:bwa PP:bamadapterclip VN:0.7.15-r1140 CL:/software/solexa/pkg/bwa/0.7.15/bwa mem -t 16 -p -Y -K 100000000 /lustre/scratch117/core/sciops_repository/references/Homo_sapiens/GRCh38_15/all/bwa0_6/Homo_sapiens.GRCh38_15.fa /tmp/DPAKaVfbyT/alntgt_bamtofastq_out @PG ID:scramble' PN:scramble PP:bwa' VN:1.14.8 CL:/software/solexa/pkg/scramble/1.14.8/bin/scramble -0 -I sam -O bam @PG ID:samtools' PN:samtools PP:scramble' VN:1.3.1-npg-Sep2016 CL:/software/solexa/pkg/samtools/1.3.1-npg-Dec2016/bin/samtools reheader /tmp/f0aBbK5Qg9/postalntgt_alterSQ_headerSQfix_out /tmp/sWIeN8pCFJ/postalntgt_mbuffer_headerSQfix_out @PG ID:bam12split PN:bam12split PP:samtools' VN:2.0.65 CL:/software/solexa/pkg/biobambam/2.0.65/bin/bam12split verbose=0 level=0 @PG ID:bamsormadup PN:bamsormadup PP:bam12split VN:2.0.65 CL:/software/solexa/pkg/biobambam/2.0.65/bin/bamsormadup threads=16 SO=queryname level=0 @PG ID:bam12auxmerge' PN:bam12auxmerge PP:bamsormadup VN:2.0.65 CL:/software/solexa/pkg/biobambam/2.0.65/bin/bam12auxmerge level=0 rankstrip=1 ranksplit=0 zztoname=0 clipreinsert=1 /tmp/MOJ8c05ONX/amp_bamadapterclip_pre_auxmerge_out @PG ID:AlignmentFilter PN:AlignmentFilter PP:bam12auxmerge' DS:Give a list of SAM/BAM files with the same set of records and in the same order but aligned with different references, split reads into different files according to alignments. 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ST:BC,FI,QT,RT,TC:1 @CO TY:checksum ST: PA:pass HA:crc32prod CO:0 BS:1 NS:1 SQ:1 ST:BC,FI,QT,RT,TC:1 @CO TY:checksum ST:22039_8#5 PA:all HA:crc32prod CO:62228666 BS:334c2975 NS:2f812f47 SQ:60b61599 ST:BC,FI,QT,RT,TC:4a187145 @CO TY:checksum ST:22039_8#5 PA:pass HA:crc32prod CO:62228666 BS:334c2975 NS:2f812f47 SQ:60b61599 ST:BC,FI,QT,RT,TC:4a187145 @SQ SN:chr1 LN:248956422 UR:/lustre/scratch117/core/sciops_repository/references/Homo_sapiens/GRCh38_15/all/fasta/Homo_sapiens.GRCh38_15.fa AS:GRCh38 M5:6aef897c3d6ff0c78aff06ac189178dd SP:Human @SQ SN:chr2 LN:242193529 UR:/lustre/scratch117/core/sciops_repository/references/Homo_sapiens/GRCh38_15/all/fasta/Homo_sapiens.GRCh38_15.fa AS:GRCh38 M5:f98db672eb0993dcfdabafe2a882905c SP:Human @SQ SN:chr3 LN:198295559 UR:/lustre/scratch117/core/sciops_repository/references/Homo_sapiens/GRCh38_15/all/fasta/Homo_sapiens.GRCh38_15.fa AS:GRCh38 M5:76635a41ea913a405ded820447d067b0 SP:Human @SQ SN:chr4 LN:190214555 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M5:2996b120a5a5e15dab6555f0bf92e374 SP:Human @SQ SN:chrUn_KI270757v1 LN:71251 UR:/lustre/scratch117/core/sciops_repository/references/Homo_sapiens/GRCh38_15/all/fasta/Homo_sapiens.GRCh38_15.fa AS:GRCh38 M5:174c73b60b41d8a1ef0fbaa4b3bdf0d3 SP:Human @SQ SN:chrUn_GL000214v1 LN:137718 UR:/lustre/scratch117/core/sciops_repository/references/Homo_sapiens/GRCh38_15/all/fasta/Homo_sapiens.GRCh38_15.fa AS:GRCh38 M5:46c2032c37f2ed899eb41c0473319a69 SP:Human @SQ SN:chrUn_KI270742v1 LN:186739 UR:/lustre/scratch117/core/sciops_repository/references/Homo_sapiens/GRCh38_15/all/fasta/Homo_sapiens.GRCh38_15.fa AS:GRCh38 M5:2f31c013a4a8301deb8ab7ed1ca1cd99 SP:Human @SQ SN:chrUn_GL000216v2 LN:176608 UR:/lustre/scratch117/core/sciops_repository/references/Homo_sapiens/GRCh38_15/all/fasta/Homo_sapiens.GRCh38_15.fa AS:GRCh38 M5:725009a7e3f5b78752b68afa922c090c SP:Human @SQ SN:chrUn_GL000218v1 LN:161147 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