Slide 1

Slide 2

Screening diseases by high- throughput sequencing ChenXiao 2015.07.261 Presented by: Xiao Chen

Slide 3

What is high-throughput sequencing? Application of high-throughput sequencing? Introduction ChenXiao 2015.07.262

Slide 4

What is ? ChenXiao 2015.07.263 Gut 2013;62:920932. doi:10.1136/gutjnl-2011-301935

Slide 5

What is ? Sequencing of millions of fragments of DNA in parallel. Mapping fragments to the human reference genome and find variation. High-throughput sequencing Massively parallel sequencing Deep sequencing Next Generation sequencing NGS ChenXiao 2015.07.264

Slide 6

454 GS FLX AB SOLiD Solexa Genome Analyzer Hiseq PGM

Slide 7

Trends in Genetics September 2014, Vol. 30, No.9. Comparison of different NGS platforms

Slide 8

ChenXiao 2015.07.267

Slide 9

Work flow of conventional versus second-generation sequencing Frederick Sanger Walter Gilbert Nature Biotechnology, 26(10):1135-1145.

Slide 10

9 DNA isolation Library preparation Sequencing Data analysis ChenXiao 2015.07.269

Slide 11

NGS APPLICATION ? Genetic diagnosis of common and rare diseases Cancer research Prenatal diagnosis Transcriptome studies Microbiological studies Evolutionary and population studies Forensics ChenXiao 2015.07.2610

Slide 12

ChenXiao 2015.07.2611 BRIEFINGS IN BIOINFORMATICS. VOL 11. NO 5. 484-498 NGS APPLICATION ?

Slide 13

Cell-free fetal DNA(cffDNA) Trophoblasts cell 10% of the DNA in maternal plasma Lancet 1997;350:485-87 Non-Invasive Prenatal Diagnosis NIPT ChenXiao 2015.07.2612

Slide 14

2014 May 20;111(20):7415-20. doi: 10.1073/pnas.1321997111. Work flow of NIPT ChenXiao 2015.07.2613

Slide 15

ChenXiao 2015.07.2614 Liao etal.PNAS, May20,2014.vol.111,no.20,7417 Z-score

Slide 16

Full sample, n Trisomy 21 sample, n False-positive rate (95% CI), % Sensitivity (95% CI), % Specificity (95% CI), %MethodReferences 18 9 0 (037)100 (63100) NGSFan et al., 2008 28 14 0 (027)100 (73100) NGSChiu et al., 2008 47 13 0 (013)100 (72100)100 (87100)NGS Sehnert et al., 2011 449 39 0.3 (0.11.5)100 (89100)99.7 (98.599.9)NGSEhrich et al., 2011 146 86 2.1 (0.66.4)100 (951)97.9 (93.699.4)NGSChiu et al., 2011 1696 212 0.2 (0.10.7)98.6 (95.9 99.7)99.8 (99.399.9)NGS Palomaki et al., 2011 298 39 0 (01.8)100 (88.81)100 (98.2100)NGSSparks et al., 2012 167 36 0 (03.6)100 (88.0100)100 (96.4100)NGSSparks et al., 2012 532 89 0 (01.1)100 (94.8100)100 (98.9100)NGS Bianchi et al., 2012 Summary of studies ChenXiao 2015.07.2615

Slide 17

T21100% (40/40)100% (372/372)100% (40/40)100% (372/372) T18100% (14/14)100% (398/398)100% (14/14)100% (398/398) T13100% (4/4)99.75% (407/408)80% (4/5)100%(407/407) T9100% (1/1)100% (411/411)100% (1/1)100% (411/411) 45X100% (5/5)99.75% (406/407)83.3% (5/6)100% (406/406) XXX100% (1/1)100% (411/411)100% (1/1)100% (411/411) XXY100% (1/1)100% (411/411)100% (1/1)100% (411/411) XYY100% (1/1)100% (411/411)100% (1/1)100% (411/411) 100%(67/67)99.71% (344/345)98.53%(67/68)100% (344/344) ChenXiao 2015.07.2616 Prenat Diagn 2013,32:1-7.

Slide 18

(+)(-)(+) (-) 6511 0 24314871* 1729 249149212 1729 (95% CI) 54.55%(24.56% 81.86%)100.00%(67.86% 100%) (95% CI) 85.95%(84.21% 87.54%)99.94%(99.63% 99.99%) FPR 14.05%0.05% FNR 45.45%0.00% PPV 2.41%94.74% Prenat Diagn. 2013 Jul;33(7):700-6. doi: 10.1002/pd.4160. Epub 2013 Jun 17. ChenXiao 2015.07.2617

Slide 19

ChenXiao 2015.07.2618 NIPT

Slide 20

ChenXiao 2015.07.2619 Thank you for your attention