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
- 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.