Ns126:Twins

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Genome-wide DNA methylation haplotype changes with smoking adjusted by genetic background[edit]

Motivation[edit]

  • Differential Effects on Homozygous Twin Astronauts Associated with Differences in Exposure to Spaceflight Factors
  • Within-pair differences of DNA methylation levels between gender groups of monozygotic twins
  • Within-pair differences of DNA methylation levels between age groups of monozygotic twins
  • 896 Paper on smoking influence to Methylome.

Background[edit]

NASA news[1]showed that only one set of twins has ever been into space, and now those twins are providing an unprecedented opportunity for scientists to understand better the effects of microgravity on the human body.

Data Analysis[edit]

Sample information[edit]

  • WGBS data for 8 pairs of twins (white blood cells)
  • Noi's experiment notes on wiki [2]
  • Mapping with BisReadMapper (BWA).
  • Trimming with TrimGalore
  • Trim/Map rates
Tube # ID# PairID Time Case/Control FastqID Total reads sequenced Total reads post trimming Total reads mapped Map rate Total CpG sites Total CpG coverage Average depth of coverage per CpG
1 27499 Twin 1 A V1 control HL_01 26,586,275 26,585,125 1,497,120 6% 115,356 1,350,354 11.71
2 27816 Twin 1 B V1 case HL_02 44,754,854 44,748,308 2,451,870 5% 218,848 2,265,242 10.35
3 28593 Twin 3 A V1 control HL_03 45,768,906 45,766,329 2,689,167 6% 254,548 2,480,837 9.75
4 29006 Twin 3 B V1 case HL_04 55,058,771 55,054,916 34,317,202 62% 9,045,133 33,467,245 3.70
5 36452 Twin 5 A V1 case HL_05 91,133,747 91,128,037 62,398,100 68% 13,440,320 58,212,675 4.33
6 36453 Twin 5 B V1 control HL_06 109,038,333 109,032,638 76,066,701 70% 17,890,575 76,099,227 4.25
7 30603 Twin 6 A V1 control HL_07 76,354,742 76,349,090 56,046,277 73% 12,957,522 52,648,864 4.06
8 30604 Twin 6 B V1 case HL_08 71,375,227 71,370,616 48,427,487 68% 11,116,087 43,359,814 3.90
9 38951 Twin 7 A V1 control HL_09 59,862,146 59,857,959 38,884,723 65% 10,803,617 36,346,952 3.36
10 38952 Twin 7 B V1 case HL_10 92,220,329 92,214,068 62,162,807 67% 14,237,896 58,043,031 4.08
11 39427 Twin 8 A V1 case HL_11 76,116,068 76,111,534 47,522,202 62% 15,658,105 47,224,187 3.02
14 32466 Twin 2 B V1 control HL_14 96,960,471 96,953,760 64,430,863 66% 19,008,006 73,095,288 3.85
15 33643 Twin 4 A V1 case HL_15 93,196,522 93,190,866 68,080,988 73% 17,803,113 65,536,853 3.68
16 33644 Twin 4 B V1 control HL_16 81,431,706 81,425,535 53,758,593 66% 13,308,886 53,103,838 3.99
12 39428 Twin 8 B V1 control HL_17 77,170,877 77,166,980 51,576,701 67% 17,910,645 55,488,885 3.10
NA NA NA NA NA HL_Un 241,815,135 241,794,233 4,514,879 2% 3,230,654 4,483,322 1.39
  • I think I need tell alan, 27499 (1A), 27816 (1B), 28593 (3A) and 29586 (2A) should be re-sequencing again.
MZ Twin Discordant for Smoking
Brinda Rana
bkrana@ucsd.edu
  • Bismark Alignment Result
Sample N(reads) N(mapped) P(mapping) N(C) N(MCPG) N(MCHG) N(MCHH) N(UCPG) N(UCHG) N(UCHH) P(MCPG) P(MCHG) P(MCHH)
HL_01.sorted.clipped 1477714 1108459 75.00% 23637043 824693 948810 3607665 155612 3828170 14272093 84.10% 19.90% 20.20%
HL_02.sorted.clipped 2441863 1829534 74.90% 40317023 1411024 1654475 6097082 242652 6574836 24336954 85.30% 20.10% 20.00%
HL_03.sorted.clipped 2678688 1996221 74.50% 43956771 1533585 1837568 6737655 270275 7084335 26493353 85.00% 20.60% 20.30%
HL_04.sorted.clipped 34314081 28852613 84.10% 670464261 21920631 3261180 7822066 5053429 139608075 492798880 81.30% 2.30% 1.60%
HL_05.sorted.clipped 62122920 52377264 84.30% 1193374135 38817548 2909480 10030944 8405045 248638493 884572625 82.20% 1.20% 1.10%
HL_06.sorted.clipped 76062942 64773878 85.20% 1582249280 50861380 2356808 7970564 12479626 332117443 1176463459 80.30% 0.70% 0.70%
HL_07.sorted.clipped 56044790 47464308 84.70% 1076856363 34838670 1454986 4931979 7636291 224852246 803142191 82.00% 0.60% 0.60%
HL_08.sorted.clipped 48419572 40649677 84.00% 904257521 28939540 1908809 6768278 5811205 185348661 675481028 83.30% 1.00% 1.00%
HL_09.sorted.clipped 38868294 32653538 84.00% 739103913 23969780 1566034 5458090 4989764 152792190 550328055 82.80% 1.00% 1.00%
HL_10.sorted.clipped 62160183 52653666 84.70% 1214507756 38953170 2785844 9737230 8601533 251303193 903126786 81.90% 1.10% 1.10%
HL_11.sorted.clipped 47519065 40446159 85.10% 975740749 31754070 2256742 7752589 7308026 203680567 722988755 81.30% 1.10% 1.10%
HL_14.sorted.clipped 64427778 55530476 86.20% 1389790947 48610649 1909269 5813780 12928265 309226163 1011302821 79.00% 0.60% 0.60%
HL_15.sorted.clipped 68078988 58107333 85.40% 1359980138 43525984 1812297 6111390 10449238 284528017 1013553212 80.60% 0.60% 0.60%
HL_16.sorted.clipped 53756332 45039147 83.80% 1029134769 34213351 1383543 4579467 8039974 217935066 762983368 81.00% 0.60% 0.60%
HL_17.sorted.clipped 51573980 43934891 85.20% 1126186881 35931209 1398364 4638953 10400033 238033195 835785127 77.60% 0.60% 0.60%
HL_Undet.sorted.clipped 4512877 3383809 75.00% 78142601 2576843 256233 705213 592919 16297940 57713453 81.30% 1.50% 1.20%
  • from above result, I can guess the bisulfite conversion of HL_01,HL_02,HL_03 failed. We need check them again.

Twins WGBS data[edit]

Sequencing[edit]

  • Alan's experiment notes on wiki [3]

Analysis[edit]

  • Fastq to fastq.gz
better to use fastq.gz to be the input (both for trim_galore and bisamrk)
qsub submit gzip job and check the err file to check whether all the compression are fine.
queue=glean
nodes=1:ppn=1, walltime=6:00:00
-rw-r--r-- 1 shg047 k4zhang-group 21194277412 Jan 12 00:13 HL_14.sorted.clipped.fastq
-rw-r--r-- 1 shg047 k4zhang-group 22411970745 Jan 12 00:17 HL_15.sorted.clipped.fastq
-rw-r--r-- 1 shg047 k4zhang-group 25034030965 Jan 12 00:20 HL_06.sorted.clipped.fastq
-rw-r--r-- 1 shg047 k4zhang-group 4535210356 Jan 12 00:20 HL_06.sorted.clipped.fastq.gz
-rw-r--r-- 1 shg047 k4zhang-group 4184336312 Jan 12 00:17 HL_15.sorted.clipped.fastq.gz
-rw-r--r-- 1 shg047 k4zhang-group 3985014694 Jan 12 00:13 HL_14.sorted.clipped.fastq.gz
* Average compression ratio (1-compressed/uncompressed): 81.2%
  • Trim_glore
trim_galore with queue=glean, nodes=1:ppn=1 and walltime=8:00:00
check the output with gzip -t 
  • Alignment with bismark
bismark choice 1: with queue=hotel, nodes=1:ppn=8, walltime=32:00:00 and multicore=2
bismark choice 2(prefer): with queue=glean, nodes=1:ppn=16, walltime=32:00:00 and multicore=4
  • Bam,bed and methylFreq files:
/media/LTS_33T/WGBS_LTS33/Hg19/HL_Rana_WGBS/BAMfiles
/media/LTS_33T/WGBS_LTS33/Hg19/HL_Rana_WGBS/BEDfiles
/media/LTS_33T/WGBS_LTS33/Hg19/HL_Rana_WGBS/MethylFreq
  • Methylation haplotype and methylation haplotype load (MHL)
/home/shg047/twin/haplotype
/home/shg047/twin/mhl

Result[edit]

Genome-wide DNA methylation haplotype change caused by smoking[edit]

  • methylation haplotype files for each samples
cd /home/shg047/work/twin
HL_01.sorted.clipped.hapInfo.txt  
HL_04.sorted.clipped.hapInfo.txt  
HL_07.sorted.clipped.hapInfo.txt  
HL_10.sorted.clipped.hapInfo.txt  
HL_16.sorted.clipped.hapInfo.txt
HL_02.sorted.clipped.hapInfo.txt  
HL_05.sorted.clipped.hapInfo.txt  
HL_08.sorted.clipped.hapInfo.txt  
HL_11.sorted.clipped.hapInfo.txt  
HL_17.sorted.clipped.hapInfo.txt
HL_03.sorted.clipped.hapInfo.txt  
HL_06.sorted.clipped.hapInfo.txt  
HL_09.sorted.clipped.hapInfo.txt  
HL_14.sorted.clipped.hapInfo.txt  
HL_Undet.sorted.clipped.hapInfo.txt
  • MHL files
    • Compare the difference with different parameter in hapinfo calling
cd /home/shg047/oasis/twin/hapinfo
perl ~/bin/hapinfo2bam

File:D802.tm.png


  • Other dataset
Epigenome-wide association study of smoking and DNA methylation in non-small cell lung neoplasms* We performed a two-stage discovery (n = 326) and validation (n = 185) analysis to investigate the association of epigenetic DNA methylation level with cigarette smoking pack-years.