Report on 3^rd series of Eminent Talks by Speakers:

Deciphering the Leukemia Genome Using Next Generation DNA Seuencing Technologies

 Date:              25/3/08

 Time:              2.15pm-4.30pm

 Venue:            KLCC convention Center

 Organizer:      Malaysia Genome Research Center (MGRC)

 Speaker:         Dr Elaine Mardis Co-director, Associate Professor of Genetics (Washington 

                        University, World’s largest Genome Research Center)

 Audience:       local universities & colleges lecturers & students, SMJK Yu Hua’s

                        6AS1,6AS2,6AS3 students lead by Pn Sang Fay Lee, Pn Rosiah Musani & En

                        Chiew Kiang Keng

 Welcome Speech by Founder of MGRC, Dr Robert Herkes

-          introduction of building blocks of genetics which is synonym to the ‘lego’ building blocks

-          the elements that build up our bodies: Hydrogen, Carbon, Oxygen, Nitrogen, Sulphur  and Phosphate( H,C,O,N,S,P)

-          H,C,O made up the glucose, H,C,O,N made up the amino acids, H,C,O,N,S, P made up the nucleic acid

-          Human genome is 4 or 5 times more than the bacteria

-          Bioengineering is the study of bio mechanism in cells through manipulation

 Introduction of Bioengineering by CEO of MGRC, Dr Iskandar Mohd Isa

-          predicted that by 2010, science will be converted into business

-          2011- 2015, expedite & intensify technology development & licensing to share to the world.

-          Scientific capability of Malaysia: at least 25 biotechnology companies are to generate 80,000 job opportunities with an estimated profit of  RM9 billion which contributes 4% of the GDP

-          Predicted that many biotechnology companies are able to achieve success earlier than 2015.

-          Example: Bio Nexus Co. has announced its talks with Hoffman Recouge to work on cancer treatment,  where the phase 2 clinical trial will be in Malaysia with its center in Cuba, U.S.A

-          There is much evidence that Malaysia is ready for bigger biotech achievements although many Malaysians are still in doubt of our abilities.

-          As Malaysians, we are able to achieve the target and we must believe we are able to work & realize it. Students are building blocks of it.

Deciphering the Leukemia Genome Using Next Generation DNA Seuencing Technologies, Dr Elaine Mardis, Washington University, U.S.A

-          The Genome Research Center of  Washington University, in St Louise, Missouri, U.S.A established in 1993

-          Through the use of the biotechnology, the cost of running the research in the university has decreased from 2001-2005.

-          The De novo genome sequences  is to study many organisms, especially cancer. The center initiated project also include study on parasites

-          The study of Human & mouse genomes has been completed but continues to close gaps & refine annotations. Besides that they are also studies on  the Y chromosome, chimp, chicken & zebra genomes, maize & microbial genomes

-          On physical mapping, they have done map construction, genome assembly, gap closure & illuminia genotyping

-          Under technology development, they have revolutionary DNA sequencing & medical sequencing

-          Platform for next generation DNA sequencing technology included: 454, Solexa, and SoliD which are faster & generate more sequencing compared to previous technology like 3730

-          454 sample preparation involve: random fragmentationà adaptor ligation àsingle stranded adaptor ligator library à anneal sDNA & oligocoated beads àemPCR for donal amplification à enrich count( each bead is coated with many sequencing reaction)

-          454 FLX evaluation is more than 100Mb data in7 hrs; read 250 bp, reading capability is 3kb separation

-          Next generation sequencing focused on diagnostic/ prohostic assays for clinic & may help identify targeted therapist for treatment

-          There is a 1,000 genomes project (www.1000genomes.org/) where the imputed genomes will be publicly available at the given web site as will all the primary data

-          Dr Elaine presented her study in PCR directed sequences in cancer which focused on whole genome tumor resequence of next generation sequencing, data analysis strategy etc.

-          Steps involved: chromosomes à sequencing à expression arrays of RNA expression, clinical data for correlation à functions in biology, targets & assays

-          Tumor sequencing project (TSP) involve 620 genes of interest, 200 lung ad neon carcinoma

-          Whole genome work with SNP,CNV & HOP

-          Found that pure KDC (PRKDC) is highly mutated, collected from 2.4 mutations/samples from non-smokers (have never smoked)

-          The hypothesis driven on kinome, phosphatone & data driver use genomic platforms to identify loci with recurrent somatic alteration

-          Acute myelogenous leukemia is AML directed sequences of FLT3 & NPM1 mutations known for whole genome sequence

-          SNP array data can be used to acquire sequences for hundreds of thousands of position across the genome & improve on the error rate

-          CDNA sequence is capable of providing rapid coverage of the interpreted genome & add information about genes expressed in the tumor

-          Next generation sequencing of DNA & RNA is for alignment on mutation detection, storage, annotation, analysis & to determine somatic status

-          The new up-coming project is on txome sequencing

-          Dr Elaine concluded her presentation by stressing that the world & Malaysia need more bioinformatics students

We were very lucky to be the only school invited to the talk for free. Many late comers had to sit on the walk way since the hall was full & no free seat. Even though most of us didn’t really understand the talk fully, we were exposed to the latest research & technology.Who knows, one day, one of us might be able to achieve this level of tertiary learning. We took our lunch before we left the school for the talk. After the high- powered talk, we were very exhausted & were lucky to be treated to tea before we left for school.