Class Notes (836,147)
Canada (509,656)
55-213 (36)
Hubberstey (25)
Lecture 8

55-213 Lecture 8 notes.pdf
Premium

7 Pages
54 Views
Unlock Document

Department
Biological Sciences
Course
55-213
Professor
Hubberstey
Semester
Winter

Description
Lecture 8 2013-02-05 3:48 AM Genomic)DNA)possibilities)for)each)SNP:) • Illumina!technology!used!to!give!you!your!SNP!sequence! • Illumina!technology!doesn’t!give!you!your!genome!sequence,!nor!an!entire!fragment! of!DNA,!rather!1!thing:!whether!AQT!or!GQC!base!pair!in!a!particular!SNP! • We!think!there!are!at!least!tens!of!millions!of!SNP!throughout!our!genomes;!some!in! genes!and!some!elsewhere! • There!are!large!stretches!of!genome!that!are!identical!in!everyone!in!this!room;! however,!there!are!other!regions,!like!in!SNPs!where!you!get!these!AQT!or!GQC! changes! • Illumina!is!an!amazing!technology:!could!etch!out!1.2!million!little!wells!which!have!a! very!tiny!droplet!containing!a!particular!primer!for!a!particular!SNP.!These!particular! primers!have!an!exact!identity!and!are!right!beside!where!the!SNP!is!going!to!be.! Primers!are!homologous!to!your!genomic!DNA!sequence!and!will!bind!there.! • There!are!only!3!cases!possible,!outlined!below.!Primer!is!green.! • See!figure!!!genomic!DNA!possibilities!for!each!SNP! ! T- ! ! C- T- A A T- T- A G C- C- G G C- ! ! primer ! DNA polymerase ! ! ! bead ! ! ! SNP #1 SNP #1 SNP #1 ! A-T homozygote A-T/C-G C-G homozygote ! heterozygote ! ! A G Genomic DNA possibilities for each SNP ! ! • In!the!first!case,!AA:! o Enzyme!in!the!droplet!will!add!a!fluorescently!labeled!T!to!the!AAs! o Chip!is!scanned!by!a!laser!which!picks!up!which!of!the!1.2!million!dots!is!the! green!one! o If!you!have!2!As!from!each!parent!at!that!spot,!the!technology!will!put!in!a!T! and!a!T.!! o Both!green,!so!it!will!up!as!green!color! o AQT!homozygote! • In!the!second!case,!AG:! o One!AT!base!pair!from!mom,!one!GC!base!pair!from!dad! o AT!will!become!green,!whereas!GC!will!become!red!(the!technology!will!have! put!in!the!T!and!the!C)! o The!computer!will!convert!these!green!and!red!colors!to!yellow!(since!green! and!red!makes!yellow)! o AQT/CQG!heterozygote! • In!the!third!case,!GG:! o If!you!have!2!Gs!from!each!parent!at!that!spot,!the!technology!will!put!in!C! and!C.!! o Both!red,!so!it!will!come!up!as!red!color! o CQG!homozygote! • The!laser!will!know!which!colored!circle!goes!where!in!your!genome!(in!what!SNP)! • This!tells!you!how!similar!all!your!DNA!is!to!each!other! • If!none!of!us!are!related!to!each!other,!it!wouldn’t!show!a!lot!of!similarity!–!due!to! having!1.2!million!nucleotides!!!massive!variation! • If!we!are!related!to!each!other,!as!siblings!for!example,!you!would!have!very!similar! SNPs! • 1.2!million!spots!on!each!slide!–!each!spot!represents!one!SNP! • The!1.2!million!dots!were!all!generated!from!known!SNP!sequences.!You!have!to! know!previous!information!before!putting!it!into!this!assay.!It!took!a!long!time!to! one SNPlion spots on each scome!up!with!these!1.2!million!SNPs.!In!fact,!we’re!continuously!coming!up!with! more!and!more!SNPs!(10!million!estimated!in!the!future).! ! 23andme:) • Carrier!Status:! o Carrier!status:!40!diseases!that!are!known!to!be!caused!by!a!mutation!or! mutations!in!a!gene! o Ex:!Cystic!fibrosis! o Professor!has!“variant!absent”!for!the!40!diseases!–!he!isn’t!a!carrier!for!any! of!them! • Family!inheritance:! o It!takes!1.2!million!SNPs!and!compares!it!to!somebody!else’s!SNP! o This!shows!you!how!related/identical!you!are!to!someone!else! o In!comparison!to!his!sister,!professor!is!50%!like!her!genetically! o Chromosome!16:!shared!no!identity!whatsoever.!This!means!she!got! different!chromosomes!from!her!parents!than!he!did!(she!got!A!and!H,!he!got! J!and!B)! o He!shares!about!a!100!million!base!pairs!of!chromosome!10!with!a!woman! named!Angela!!!this!means!at!one!point,!they!shared!a!common!ancestor!! • Google!owns!it! o Objective:!get!1!million!subscribers!by!end!of!this!year.! o Current!status:!250!000!subscribers! ) Microarray)(DNA)chip))Technology:! • Every!gene!from!organism!is!spotted!onto!glass!slide!(titling!array)! • Different!from!Illumina!technology,!but!there!are!similarities!!!they!both!give!you! red,!green!or!yellow!colors! • Every!spot!on!a!microarray!is!a!sequence/of/DNA!that!represents!a!gene! • So!if!you!had!every!gene!spotted,!how!many!spots!would!you!have?!25!000,!whereas! Illumina!had!1.2!million!! • mRNA!is!isolated!from!different!tissues!and!cDNA!is!made!with!fluorescently!labeled! nucleotides! • 1998:!this!was!presented!at!a!major!conference!! • Labeled!cDNA!from!different!tissues!is!used!to!probe!slide!(e.g.!cancer!vs.!normal)! • You!isolate!mRNA!from!different!tissues,!make!cDNA,!add!fluorescently!labeled! nucleotides!! • Afterwards,!look!at!expression!pattern! • Can!take!liver!cancer!cells!and!normal!cells!and!label!them!with!different!colors!in! order!to!try!to!see!what!is!being!expressed!in!cancer!cells!but!not!in!normal!cells!(or! vice!versa)! • Hybridization!needs!to!work!! • Differences!in!gene!expression!between!tissues!can!be!measured! • This!gives!you!the!power!of!looking!at!the!entire!expression!profile!of!a!particular! tissue!at!a!particular!time! • See!figure!3.24! o If!it!was!genomic!DNA,!you!would!only!get!hybridization!in!coding!regions! and!it!would!make!a!massive!difference!due!to!the!presence!of!introns! o Computer!gives!ratios!of!color! o Oligonucleotide:!synthetic!sequence!of!DNA! ! ! ! ! ! ! ! ! ! ! ! ! ! ! ! ! ! ! ! ! ! ! ! ! ! ! ! ! ! ! ! ! ! ! ! • These!chips!have!24!000!genes!o
More Less

Related notes for 55-213

Log In


OR

Join OneClass

Access over 10 million pages of study
documents for 1.3 million courses.

Sign up

Join to view


OR

By registering, I agree to the Terms and Privacy Policies
Already have an account?
Just a few more details

So we can recommend you notes for your school.

Reset Password

Please enter below the email address you registered with and we will send you a link to reset your password.

Add your courses

Get notes from the top students in your class.


Submit