Supplementary Data
Whole exome sequencing in an Indian family links cerebroretinal microangiopathy with
calcifications and cysts(CRMCC) and dextrocardia with a homozygous novel CTC1 and
a rare HES7 variation
Manjunath Netravathi1, Saketh Kapoor2, Renu Kumari3, Pushkar Dakle3, Manish Kumar
Dwivedi3, Sumit Deb Roy4, Paritosh Pandey5, Jitender Saini6, Anil Ramakrishna1 , Devaraddi
Navalli1, Parthasarathy Satishchandra1, Pramod Kumar Pal1* , Mohammed Faruq3* and Arun
Kumar2*
1
Department of Neurology, National Institute of Mental Health and Neuro Sciences,
Bangalore, India.
2
Department of Molecular Reproduction, Development and Genetics, Indian Institute of
Science, Bangalore, India.
3
Genomics and Molecular Medicine, CSIR-Institute of Genomics and Integrative Biology,
Mall Road, New Delhi, India.
4
Proteomics and Structural Biology Unit, CSIR-Institute of Genomics and Integrative
Biology, Mall Road, New Delhi, India.
5
Department of Neurosurgery, National Institute of Mental Health and Neuro Sciences,
Bangalore, India.
6
Department of Neuroimaging and Interventional Radiology, National Institute of Mental
Health and Neuro Sciences, Bangalore, India.
Supplementary materials and methods
Genetic analysis of the family
Following informed consent, 3-5 ml of the peripheral blood sample was collected from
proband(case:II-1) and both the parents in a Vacutainer EDTA™ tube (Beckton-Dickinson,
Franklin Lakes, NJ) for genomic DNA isolation using a Wizard™ Genomic DNA
Purification Kit (Promega, Madison, WI). This research followed the tenets of the
Declaration of Helsinki and the guidelines of the Indian Council of Medical Research, New
Delhi.
Targeted resequencing of CTC1
For mutation screening, the entire coding region and intron-exon junctions of the CTC1 gene
(GenBank NM_025099.5) were amplified by polymerase chain reaction with appropriate
primer pairs (Table S1). The amplified PCR products were subjected to Sanger sequencing
followed by analysis on an ABIprism A370-automated sequencer (PE Biosystems, Foster
City, CA). Once the mutation was identified, both parents were also examined for the
presence of the mutation by sequencing. A total of 50 normal controls were examined for the
presence of the mutation by DNA sequencing.
Whole exome sequencing
Whole exome sequencing was carried out in 3 individuals of this family comprising the
proband and both the parents. For exome sequencing, 2 μg of DNA was used for
fragmentation, and DNA library preparation was carried out according to Illumina DNA
sample prep protocol.v2. Exonic regions were captured and enriched using Truseq Illumina
exome capture kit.v2 protocol. Cluster generation using cBOT was carried out for exome
enriched libraries on Illumina flow cell.v3 followed by 100bp paired end sequencing on
Hiseq2000 using Illumina SBS kit.v3 protocol. Nearly 12 Gb raw data was generated for each
sample. The base calls for all the sample reads were analyzed on CASAVA and subsequent
pipeline for data processing is described in the following section. The validation of selected
candidate variation for dextrocardia (HES7, rs182882481) from exome analysis was carried
out by Sanger sequencing using Big-Dye terminator sequencing kit on 3130xl sequencer
(ABI, Foster City).
Exome sequence analysis
Paired-end raw sequencing reads of length 101 bp were trimmed to 96 bp using
Trimmomatic1
based
on
the
quality
score
assessment
by
FastQC
[http://www.bioinformatics.babraham.ac.uk/projects/fastqc/]. These reads were further
trimmed if the phred quality score dropped below 20 for a window of 25 bases. For subject,
I-2(pedigree chart, Fig. 1, i), the raw reads were trimmed with a more stringent cutoff of
phred score dropping below 30 in a window of 10 bases. Finally, the reads which were of
length greater than 50bp were taken forward. The filtered reads were then aligned against
human genome reference (human.g1k.v37.fasta) using Stampy2. PCR duplicates were labeled
in aligned reads using Picard Markduplicates (http://picard.sourceforge.net/).
Genome Analysis toolkit (GATK) from http://www.broadinstitute.org/gatk was used to
realign BAM file around indels and further scores were re-calibrated to obtain final processed
BAM file. Variant calls were made jointly for all the samples using Unified Genotyper
module of GATK3. Raw calls were labeled using GATK's VariantAnnotator based on filter
expressions. SeattleSeqAnnotation138 server was used to further annotate the calls based on
their
genomic
location–
genic/non-genic
and
their
effect(http://snp.gs.washington.edu/SeattleSeqAnnotation138/).
Analysis of variations in the known candidate genes from WES data
The variation data was obtained for 15 genes involved in telomere length maintenance
activity(TERF2IP,POT1,TERF1,OBFC1/STN1,CTC1,TERT,DKC1,WRAP53,TINF2,TPP1,T
ERF2,TEN1,TERC,NHP2 and NOP10). All the known and novel variations passing quality
filter criterias of GATK were considered for the further analysis(n=23 variations) of direct or
indirect association. For Dextrocardia phenotype, a total of 111 variations were obtained from
28 known candidate genes; ACVR2B, CCDC103, CRELD1, DNAH11, GATA4, HES7,
MEGF8, NODAL, PKD2, PRKAR1A, SMAD2, CCDC11, INVS, NPHP3, DNAI1, DNAAF1,
CCDC114, DYX1C1, CLMP, UBR1, SCN5A, B9D1, CFC1, DNAAF3, ZIC3, MBS1, GDF1,
ZMYND10 (supplementary TableS4). All dextrocardia genes related variations were also
analyzed with autosomal recessive inheritance pattern to document their potential association
with the phenotype (supplementary Table S5).
Whole exome variants analysis and variant filtering
For a stringent and unbiased approach to analyze the whole exome variations in this family,
we filtered variations in the following manner. All calls that were reported in dbsnp138
(http://www.ncbi.nlm.nih.gov/projects/SNP/index.html) were removed.
Only protein
damaging variations, such as non-synonymous, stop-gain or loss, splice site and indels, were
further used to locate variations/gene that fit the model of recessive inheritance i.e genes with
homozygous or compound heterozygous mutations in same gene.
Finally, these calls were predicted for their role in pathogenicity using SIFT
(http://sift.jcvi.org), Polyphen-2 algorithm (http://genetics.bwh.harvard.edu/pph2/) and
Mutation Taster (www.mutationtaster.org/). To find the functional significance of the
mutated amino acid residue, CTC1 protein sequences from different species were aligned by
the ClustalW2 program (http://www.ebi.ac.uk/Tools/msa/clustalw2/).
To predict the effect of the mutation on CTC1 function, we used two bioinformatics
programs:
Mutation
Taster
(http://www.mutationtaster.org)
and
PolyPhen-2
(http://genetics.bwh.harvard.edu/pph2/). The output from the Mutation Taster program is a p
(probability) value. A p value close to 1 indicates a high 'security' of prediction function. The
output score from the PolyPhen-2 program ranges from 0 to a positive number, where 0 is
neutral, and a high positive number is damaging to protein function.
Supplementary Table S1: Details of PCR primers used in the mutation analysis of CTC1.
Exon
Primer Sequence (5’ to 3’)
Tm (°C)
1
F:CCTCGCGGAGTCTCTAGGAAGCGAG
R:ACAACCCCCTCACCCATGGGCCGGA
F:CCGGCCCGGATATTTTTTTCTAGTC
R:AGACTACCTTGTCCTCCGCTCAC
F:ATGTTCCCTGCAACCTTTCCCTG
R:ACCTCCCCGTTTGTTTCCTCAG
F:CAAGAATGGTGTCCAAGGATCAAGGCA
R:TCAAAGCCCACCATTCCCTTGATTTGGA
F:TGAGACGTAGTTTCACTCCTGCTGC
R:TCCTACATGGCTCCTCCTATGATGC
F:GTCTCTGAGTTCAAATCGTGAGG
R:ATTTCTATATAACCACCCTGCTGC
F:GGCAGTGGCAAAGTGCGGTTAACTC
R:GAGCCTGCCTCTTCAAGAATCCTGC
F:CAGTGGGAGTAGCACACTTCCTTGG
R:ATGACGAAGAAAGATAGTAACCGAGAC
F:AGCTTTACCATGTAATACAGCATCTGG
R:TCTGCATCTCTAGTAAATCCCAGCAG
F:GTGAGGCCGGTAGGATGGTTTGC
R:ACTGGACATAGACTCTGTTGGGAG
F:TCCTTGGGGTCATGGTTGTCTTGAG
R:AGGCCTAGAGAATGACCAGGCACTG
F:CAGTGCCTGGTCATTCTCTAGGCCTC
R:CTTCACCAAACCCAGCTAGCTTGGGA
F:TGAAGTTCTAGCAGATACTTTAGCTCCA
R:TATGAAAGAGAAGGGGTCGCTGCAG
F:CCATGGCTAGGATATGTCCCTCAG
R:GGATTGGAGAAGACTGTAATGATGG
F:CTCTAAGTCCTTCTAGACCCAC
R:TTCTCATGAGCCAGGAATTATGC
F:GTGAGCCAAAGACTGCAGACAGC
R:GAAATTCCCCATCAGTCCCTCATC
F:GATGAGGGACTGATGGGGAATTTC
R:CTGGAGTCCTTGGTTCAATCACAGA
F: GTAGGAGCCAGGAGTTGCA
R: TTGGCAAGGAGAGCAGGATT
IP: GCTCCCAGGAGAGGAATGTT
62
Amplicon
size (bp)
321
62
381
62
443
62
460
62
384
62
700
62
410
62
659
62
322
62
346
62
724
62
453
59
567
62
306
62
495
62
595
62
349
60
164
2
3
4
5
6+7
8
9+10
11
12
13+14
15
16+17
18
19+20
21+22
23
Genotyping
primer* for
p.H484P
variation

*Genotyping was done by SNaPshot reaction kit (ABI) which is based on single base extension
chemistry. F, forward primer; R, reverse primer; IP, Internal primer targeted penultimate to the
variation of interest.
Supplementary Table S2: Details of Exome sequencing with respect to read counts, depth of
coverage and mapping statistics for each DNA sample sequenced.
Sample ID
Raw
Reads
Filtered
Reads
II-1(Proband)
I-1(Father)
I-2(Mother)
71486240
63329178
67592800
66121038
57945272
29144024
Alignment
(Properly
Paired)
99.64%
99.21%
99.50%
mean
depth
59.56
50.60
22.12
Percentage of Exome
with non zero coverage
(per base)
95.05
94.93
93.48
Supplementary Table S3: Variation analysis of known telomere associated genes.
Genomic coordinates
chr17:g.8138233T>G
chr17:g.8129160A>G
chr17:g.8132763T>C
chr17:g.8135061T>C
chr17:g.7606723GC>G
chr15:g.34634033A>G
chr15:g.34634124C>G
chr15:g.34634138G>A
chr15:g.34634139T>C
chr10:g.105638232T>C
chr10:g.105640978C>T
chr10:g.105641935G>GCAAGTGA
chr10:g.105657316G>C
chr10:g.105659826T>C
chr7:g.124462655T>C
chr7:g.124462661C>T
chr8:g.73958718G>A
chr16:g.75681743C>G
chr16:g.75691252A>G
chr5:g.1268721C>T
chr5:g.1294086C>T
chrX:g.153994596G>T
chrX:g.154005148G>A
Variation
status
Novel
rs8078338
rs3826543
rs3027238
rs373064567
rs3063
rs1045238
rs1045204
rs1045194
rs4917405
rs7100920
rs147944736
rs10786775
rs2487999
rs76436625
rs17246404
rs10112752
rs1865493
Novel
Novel
rs2736098
rs2728532
rs1800533
GL
CTC1
CTC1
CTC1
CTC1
WRAP53
NOP10
NOP10
NOP10
NOP10
OBFC1
OBFC1
OBFC1
OBFC1
OBFC1
POT1
POT1
TERF1
TERF2IP
TERF2IP
TERT
TERT
DKC1
DKC1
FG
II-1
missense
1/1
3'UTR
0/0
missense
0/0
missense
1/1
frameshift
0/0
3'UTR
0/1
3'UTR
0/1
3'UTR
0/1
3'UTR
0/1
3'UTR
1/1
3'UTR
0/1
3'UTR
0/1
missense
1/1
missense
1/1
3'UTR
0/0
3'UTR
0/1
3'UTR
0/0
5'UTR
0/1
3'UTR
0/0
synonymous 0/1
synonymous 0/1
synonymous 1/3'UTR
1/-
I-1
0/1
0/0
0/0
1/1
0/0
0/1
0/1
0/1
0/1
1/1
0/1
0/1
1/1
1/1
0/0
0/0
0/0
0/1
0/1
0/1
1/1
1/0/-
I-2
0/1
0/1
0/1
1/1
0/1
0/0
0/0
0/0
0/0
1/1
1/1
1/1
1/1
1/1
0/1
0/1
0/1
0/1
0/0
0/0
0/0
1/1
0/1
Supplementary Table S4: WES variations from known Dextrocardia/situs-inversus
associated genes.
Coordinates
chr3:38519424 A>G
chr3:38524742 C>T
chr3:38525567 T>C
chr3:38525734 C>T
chr3:38525864 A>C
chr3:38526166 CAA>C
chr3:38527215 T>C
chr3:38527913 C>T
chr3:38528537 G>T
chr3:38529440 C>G
chr3:38529818 C>T
chr3:38529825 C>T
chr3:38531211 T>G
chr3:38532511 G>A
chr3:38533335 A>C
chr3:38534133 T>TA
chr17:42980189 G>A
chr18:47777323 T>C
chr19:48799716 A>G
chr11:122943495 T>C
chr11:122944081 C>CCT
chr11:123065902 A>G
chr3:9976159 A>G
chr3:9987049 A>G
chr16:84203612 A>G
chr16:84203730 G>C
chr16:84203939 C>T
chr16:84209634 C>G
chr16:84209738 T>C
chr16:84209816 T>C
chr16:84209864 G>C
chr7:21582963 G>T
chr7:21582964 A>T
chr7:21598500 A>G
chr7:21599233 C>T
chr7:21603886 A>G
chr7:21628197 A>G
chr7:21628237 C>T
chr7:21628242 C>G
dbSNP
rs2070489
rs1046048
rs7642472
rs6599204
rs7640050
rs56291663
rs11914389
rs11926767
rs928813
rs6599205
rs7433277
rs2370840
rs7374458
rs1058945
rs13072731
rs34717882
rs8079308
Novel
rs2292112
rs7949414
rs149599709
rs3132824
rs279552
rs73118375
rs17856705
rs9972733
rs11644164
rs2288019
rs2288020
rs2288022
rs2288023
rs2285943
rs2285944
rs72655972
rs10950854
rs4392792
rs12670130
rs6963535
rs62441683
Gene
ACVR2B
ACVR2B
ACVR2B
ACVR2B
ACVR2B
ACVR2B
ACVR2B
ACVR2B
ACVR2B
ACVR2B
ACVR2B
ACVR2B
ACVR2B
ACVR2B
ACVR2B
ACVR2B
CCDC103
CCDC11
CCDC114
CLMP
CLMP
CLMP
CRELD1
CRELD1
DNAAF1
DNAAF1
DNAAF1
DNAAF1
DNAAF1
DNAAF1
DNAAF1
DNAH11
DNAH11
DNAH11
DNAH11
DNAH11
DNAH11
DNAH11
DNAH11
II-1
1/1
1/1
1/1
1/1
1/1
1/1
1/1
1/1
1/1
1/1
1/1
1/1
1/1
1/1
1/1
1/1
0/1
0/0
0/1
0/0
0/0
1/1
1/1
1/1
0/1
0/0
0/1
0/1
0/1
0/1
0/1
0/0
0/0
0/0
0/1
0/1
0/0
1/1
0/0
I-1
1/1
1/1
1/1
1/1
1/1
1/1
1/1
1/1
1/1
1/1
1/1
1/1
1/1
1/1
1/1
1/1
0/0
0/1
0/0
0/1
0/1
1/1
1/1
1/1
0/1
0/1
0/1
0/1
0/1
0/1
0/1
0/0
0/0
0/0
1/1
0/1
0/1
1/1
0/1
I-2
1/1
1/1
1/1
1/1
1/1
1/1
1/1
1/1
1/1
1/1
1/1
1/1
1/1
1/1
1/1
1/1
1/1
0/0
0/1
0/0
0/0
1/1
1/1
-/0/1
0/0
0/1
0/1
0/1
0/1
0/1
0/1
0/1
0/1
0/1
0/0
0/0
1/1
0/0
chr7:21630982 A>G
chr7:21640361 T>C
chr7:21640405 A>G
chr7:21641218 G>A
chr7:21659645 T>C
chr7:21765452 C>T
chr7:21775443 G>A
chr7:21778449 C>T
chr7:21779278 A>G
chr7:21824058 A>G
chr7:21893993 G>T
chr7:21901566 T>C
chr7:21924014 A>G
chr7:21932044 C>T
chr9:34500821 G>A
chr8:11614575 A>G
chr8:11616338 A>C
chr8:11616410 C>T
chr8:11616501 T>C
chr8:11616516 T>C
chr8:11616547 C>G
chr8:11616571 A>G
chr8:11616836 G>A
chr8:11617240 A>T
chr17:8024121 C>T
chr17:8024204 T>C
chr17:8024237 T>C
chr17:8024333 T>C
chr17:8024758 C>A
chr9:102861613 T>G
chr9:103063253 A>G
chr19:42882829 TA>T
chr10:72191952 A>G
chr10:72191970 C>G
chr10:72195439 T>C
chr10:72195576 G>A
chr10:72201294 T>G
chr4:88997021 A>AT
chr4:88997102 C>T
chr17:66527262 T>C
chr17:66527402 A>C
chr17:66527834 T>C
chr17:66528367 C>T
chr17:66528778 C>G
chr3:38589666
T>TCCCTCCTTTTTCCTA
rs4615458
rs10269582
rs10224537
rs3827657
rs56029521
rs12536928
rs2072221
rs1109806
rs9639393
Novel
rs4722064
rs4722067
rs6461613
rs12537531
rs11793196
rs3729856
rs867858
rs1062219
rs884662
rs904018
rs12825
rs804291
rs804290
rs12458
rs1442849
rs75711247
rs1442850
rs182882481
rs114049508
rs7024375
rs190277417
rs3214618
rs2279253
rs2279254
rs1904589
rs77151171
Novel
Novel
rs2728121
Novel
rs116996069
rs9925
rs7977
rs6958
DNAH11
DNAH11
DNAH11
DNAH11
DNAH11
DNAH11
DNAH11
DNAH11
DNAH11
DNAH11
DNAH11
DNAH11
DNAH11
DNAH11
DNAI1
GATA4
GATA4
GATA4
GATA4
GATA4
GATA4
GATA4
GATA4
GATA4
HES7
HES7
HES7
HES7
HES7
INVS
INVS
MEGF8
NODAL
NODAL
NODAL
NODAL
NODAL
PKD2
PKD2
PRKAR1A
PRKAR1A
PRKAR1A
PRKAR1A
PRKAR1A
0/0
0/1
0/1
0/1
0/1
1/1
1/1
0/1
0/1
0/0
0/1
0/1
1/1
1/1
0/1
0/1
1/1
0/0
0/0
1/1
1/1
1/1
0/0
1/1
1/1
0/0
1/1
1/1
0/0
0/1
0/0
0/1
0/1
0/1
1/1
0/0
0/0
0/1
0/1
0/1
0/0
0/1
0/1
0/1
0/1
0/0
0/1
0/1
0/1
1/1
0/1
0/0
0/0
0/1
0/0
0/1
1/1
1/1
0/0
0/0
0/1
0/1
0/1
1/1
0/1
1/1
0/1
0/1
1/1
0/1
1/1
0/1
0/0
0/1
0/1
1/1
0/1
0/1
1/1
0/0
0/0
0/0
0/0
0/0
0/0
0/0
0/0
1/1
0/1
0/1
1/1
1/1
0/1
0/1
1/1
1/1
1/1
0/0
0/1
1/1
1/1
1/1
0/1
0/1
0/1
0/1
0/1
1/1
0/1
1/1
0/1
0/1
0/1
0/0
1/1
0/1
0/1
0/1
0/0
0/0
0/0
0/0
0/1
0/1
0/1
1/1
1/1
0/1
0/1
1/1
0/1
0/1
rs45592631
SCN5A
1/1
1/1
1/1
CTCTCTTCTC
chr3:38590358 C>CT
chr3:38590470 A>G
chr3:38590849 G>A
chr3:38590850 A>T
chr3:38591059 G>A
chr3:38591689 T>C
chr3:38592406 A>G
chr3:38622467 T>C
chr3:38645420 T>C
chr3:38674712 T>C
chr18:45359664 T>A
chr18:45360991 A>G
chr18:45361016 C>CTTAT
chr18:45362150 C>A
chr18:45362194 T>C
chr18:45363214 A>T
chr18:45365396 CA>C
chr18:45367484 A>G
chr15:43236612 C>T
chr15:43237203 T>C
chr15:43237572 T>C
chr19:55671337 C>T
chr19:55671374 C>T
chr19:55672055 A>G
chr19:55673145 C>T
chr19:55673164 T>C
chr19:55673654 T>C
rs11414422
Novel
rs4073796
rs4073797
rs41310757
rs7429945
rs1805126
rs7430407
rs1805124
rs6599230
rs8671
rs1981
rs111850625
Novel
rs1792671
rs1792666
rs5824709
rs1787187
rs7178567
rs3803341
rs16957277
rs890872
rs891187
rs890871
rs58824375
rs56726774
rs3848618
SCN5A
SCN5A
SCN5A
SCN5A
SCN5A
SCN5A
SCN5A
SCN5A
SCN5A
SCN5A
SMAD2
SMAD2
SMAD2
SMAD2
SMAD2
SMAD2
SMAD2
SMAD2
UBR1
UBR1
UBR1
DNAAF3
DNAAF3
DNAAF3
DNAAF3
DNAAF3
DNAAF3
0/1
0/1
0/1
0/1
0/1
0/1
0/1
1/1
0/1
0/1
1/1
1/1
1/1
0/0
1/1
1/1
1/1
1/1
1/1
1/1
0/1
1/1
0/1
0/1
0/1
0/1
0/1
0/0
0/1
0/0
0/0
0/0
0/0
0/0
1/1
0/1
1/1
0/1
0/1
1/1
0/1
0/1
0/1
0/1
1/1
1/1
1/1
0/1
1/1
0/0
0/1
0/1
0/1
1/1
0/1
0/0
0/1
0/1
0/1
0/1
0/1
1/1
0/0
0/1
0/1
0/1
1/1
0/0
0/1
0/1
0/1
1/1
1/1
1/1
1/1
1/1
0/1
0/0
0/0
0/0
0/0
Supplementary Table S5: Variation analysis of known candidate of dextrocardia phenotype
with homozygous disease model.
Genomic coordinates
chr17:g.8024333T>C
chr8:g.11616338A>C
chr8:g.11616547C>G
chr8:g.11617240A>T
chr18:g.45359664T>A
chr18:g.45360991A>G
chr18:g.45362194T>C
chr18:g.45363214A>T
chr18:g.45365396CA>C
variation
status
rs182882481
rs867858
rs12825
rs12458
rs8671
rs1981
rs1792671
rs1792666
rs5824709
Gene
HES7
GATA4
GATA4
GATA4
SMAD2
SMAD2
SMAD2
SMAD2
SMAD2
Location
3'UTR
3'UTR
3'UTR
3'UTR
3'UTR
3'UTR
3'UTR
3'UTR
3'UTR
II-1
1/1
1/1
1/1
1/1
1/1
1/1
1/1
1/1
1/1
I-1
0/1
0/1
0/1
0/1
0/1
0/1
0/1
0/1
0/1
I-2
0/1
0/1
0/1
0/1
0/1
0/1
0/1
0/1
0/1
TGP
MAF
0.001
0.358
0.453
0.392
0.423
0.385
0.384
0.423
0.66
Supplementary Table S6: Compound heterozygous model WES data.
Genomic coordinate
chr11: g.6540998 G>T
chr11: g.6585264
C>CCT
chr14: g.105223033 G>A
chr14: g.105223055 G>T
chr7: g.151896438 T>A
chr7: g.151917753 G>T
Gene
Effect
DNHD1 missense
II-1
0/1
I-1
0/0
I-2
0/1
DNHD1
SIVA1
SIVA1
KMT2C
KMT2C
0/1
0/1
0/1
0/1
0/1
0/1
0/1
0/0
0/1
0/0
0/0
0/0
0/1
0/0
0/1
frameshift
missense
missense
missense
missense
Supplementary Table S7: The variation found in the homozygous stretch on chr17.
Genomic coordinates
chr17:g.6942111 G>T
chr17:g.7224921 C>G
chr17:g.7257185 C>T
chr17:g.7257669 C>A
chr17:g.7257847
GGT>G
chr17:g.7360110 T>C
chr17:g.7363055 A>G
chr17:g.7369541 C>T
chr17:g.7460517 G>C
chr17:g.7554536 T>C,G
chr17:g.7554772 C>T
chr17:g.7560294 C>T
chr17:g.7836105 G>A
chr17:g.7942434 A>G
chr17:g.8024333 T>C
chr17:g.8048216 C>T
chr17:g.8062993 G>A
chr17:g.8138233 T>G
chr17:g.8222870 C>T
chr17:g.8224276 T>C
chr17:g.8224670 G>C
chr17:g.8225768 A>G
chr17:g.8225787 C>T
chr17:g.8243661 G>A
chr17:g.8243785 A>G
chr17:g.8272767 G>A
chr17:g.8701116 G>A
chr17:g.8702205 C>T
chr17:g.9674901 C>T
chr17:g.9674922 A>G
chr17:g.9674976 T>C
ID
rs33979567
rs3809813
rs3809830
rs3809831
Gene
SLC16A13
NEURL4
KCTD11
KCTD11
effect
synonymous
missense
3'UTR
3'UTR
rs3840878
rs2302764
rs371972614
Novel
rs3803798
rs1050528
rs1642762
rs1050533
rs72841443
rs73972649
rs182882481
Novel
rs75056600
Novel
rs79993581
rs3744647
rs1045161
rs1045172
rs2430
rs12601097
rs12936935
rs2430949
rs2242374
Novel
rs114469918
rs11654889
rs11655932
KCTD11
CHRNB1
ZBTB4
ZBTB4
TNFSF12/TNFSF12-TNFSF13
ATP1B2
ATP1B2
ATP1B2
CNTROB
ALOX15B
HES7
PER1
VAMP2
CTC1
ARHGEF15
ARHGEF15
ARHGEF15
ARHGEF15
ARHGEF15
ODF4
ODF4
KRBA2
MFSD6L
MFSD6L
DHRS7C
DHRS7C
DHRS7C
3'UTR
3'UTR
3'UTR
missense
synonymous
5'UTR
5'UTR
3'UTR
5'UTR
5'UTR
3'UTR
missense
3'UTR
missense
missense
missense
3'UTR
3'UTR
3'UTR
missense
missense
synonymous
synonymous
synonymous
synonymous
synonymous
synonymous
References
1.
Bolger, A., Lohse, M. and Usadel, B. Trimmomatic: a flexible trimmer for Illumina
sequence data. Bioinformatics, 2014 p.170
2. Lunter G, Goodson M. Stampy: a statistical algorithm for sensitive and fast mapping
of Illumina sequence reads. Genome Res 2011;21:936-9
3. McKenna A, Hanna M, Banks E, et al. The Genome Analysis Toolkit: a MapReduce
framework for analyzing next-generation DNA sequencing data. Genome Res
2010;20:1297-303.