Lecture 1: Dr.Hu Flashcards
How big is the human genome?
- 3.2 billion bases per haplotype
- ^.4 billion bases in a diploid cell
How many genes do we have?
- Estimated ~20,000-25,000 protein coding genes, comprised of 1.5% of our genome
- Rest made up of non-coding sequences or so called “junk DNA”
How many bases is 1 killobase (Kb)?
1,000 bases
How many bases is 1 megabase (Mb)
it is 1,000,000 bases or one thousand kilobases or 100x1000
- 1 million bases of sequencing data is equivalent to 1/4 megabyte of computer data (RAW DATA) ~ does not include other annotations or other information
- 3 billion nucleotides genome is equivalent to 3/4 gigabytes of computer data and full diploid sequence is 1.5 terabytes.
What is the average gene?
5Kb pre-mRNA
Big genes are
over 500kb pre-mRNA
- 200 or so genes have been identified so far
- Mainly found in the CNS related developmental sites
- Chromosomal instabilities sites
Genes can be as small as?
a single exon ex.) histone genes or as big as the dystrophin gene with 79 exons spanning 2.4 Mb
What is the average exon size?
150-200 bp
- However exon 26 of the apoB gene (APOB) is 7.6 kb, exon 15 of the adenomataous polyposis coli gene (APC) 6.5 kb, exon 11 of the BRCA1 Breast cancer gene is 3.4 kb
What is the intron size?
0.5 kb to 30kb
What is mRNA size
2.2kb
What size is 5’UTR
~100 bases
What size is the coding DNA?
1.5-1.8kb or 500-600 codon
What size is 3’ UTR
600-800 bases
How is chromosomes abnormalities defined
as changes resulting in a visible alteration of the chromosome
- Banding pattern can reveal structures that are 1-10 Mb regions
- smallest loss or gain of material visible by traditional methods on standard cytogenetics is ~4 megabases of DNA
Fluorescent instu hybridization characteristics
- 100-400 kb probes (commercial)
- 70kb (home brew)
Array comparative genomic hybridization (aCGH)
genomic copy number differences 5-10 kb
Oligonucleotide arrays or DNA arrays use?
uses 25 nucleotide length probes
Gene chip microarray use?
use 7 base sequence
What are the types of chromosomal abnormality?
- Constitutional abnormality: sperm or egg, early embryo post fertilization
- Somatic or acquired abnormality
- Two categories: structural and numerical
What are the causes of aneuploidy?
Nondisjunction and anaphase lag
What is nondisjunction?
It is the failure of paired chromosomes to separate or disjoin in anaphase of meiosis 1 or failure of sister chromatids to disjoin at either meiosis 2 or at mitosis
- Nondisjunction in meiosis produces gametes with 22 or monosomic zygote.
- Nondisjunction in mitosis produces a mosaic (mixoploidy)
What is anaphase lag?
It i the failure of chromosome or chromatid to be incorporated into one of the daughter nuclei following cell division as a result of delay movement (lagging) during anaphase.
-Chromosomes that do not enter a daughter cell nucleus are lost
What is mixoploidy?
It includes mosaicism which is an individual that possesses two or more genetically different cell lines all derived from a single zygote
- Chimerism which is an induvial who has two or more genetically different cell lines originating from different zygotes. Abnormalities that would be lethal in constitutional form may be compatible with life in mosaics which is very rare.
Balanced translocations involve?
involves 2 chromosomes - 46,xx,t(8;14)(q24;q12) example: Tumor suppression Involving 3 chromosomes -46,xx,t(8;22;14)(q24;q11;q12) example: Leukemia and lymphoma's
Unbalanced Translocations are
Robertsonian translocations, constitutional studies only, 45,XX,rob(14;21)(q10;q10)
For Robertsonian translocation key factors to under
- Chromosomal rearrangement between the 5 acrocentric chromosome pairs
- 13,14,15,21,22
ex. Forensics is how it is commercialized
Derivative chromosome are
Generated by more than one aberration within a single chromosome or rearrangement involving two or more chromosomes (multiple abnormalities on one chromosome)
- 46,xx,der(7)add(7)(p22)del(7)(q22q34
- 46,xy,der(9)inv(9)(p11q12)t(9;22)(q34;q11.2),der(22)t(9;22)
Insertions
-Direct: 46,XY,ins(5)(q14q21q31) intra
46,XY,ins(5;1)(q14;q22q32) inter
-Inverted: 46,XY,ins(5)(q14q31q21)
46,XY,ins(5;1)(q14;q32q22)
Deletions
-Terminal Deletions
46,XX,del(7)(p11)
-Interstitial Deletions
46,XX,del(5)(q13q33)
Duplication
-Terminal Deletions
46,XX,del(7)(p11)
-Interstitial Deletions
46,XX,del(5)(q13q33)
Isochromosomes and rings
-Isochromosomes
46,XX,i(17)(q10)
-Rings
46,XX,r(4)(p14q31)
Clonal evolution is
- Observed in cancer
- Parallels that of Darwinian natural selection: it is a diversification process of which occurrence depends on the ecosystem it s in
- 1st published in 1976 by peter nowell in his landmark paper on cancer evaluation: stepwise, somatic cell mutations with sequential sub clonal selection.
Composite Karyotype
- great karyotypic heterogeneity within tumor population
- common changes but no two cells share the same structural and numerical aberrations.
Examples of chimerism?
- Bone marrow transplant
- Fetal cell envelopment by mother
- Twin absorbing the other twin
Composite Karyotype (CP) ex.)
45,XX,-15,del(17)(q11.1) 46,XX,+7,-15,del(17)(q11.1) 46,XX,+12,-15 47,XX,+7 47,XX,+15,del(17)(q11.1) 48,XX,+12,+15 Composite karyotype will be: 45~48,XX,+7,+12,+15,-15,del(17)(q11.1)[cp6]
Ploid range
- 23+/- 11= 12 - 34 haploid range
- 46+/- 11= 35 - 57 diploid range
- 69+/- 11= 58 - 80 triploid range
- 92+/- 11= 81 - 103 tetraploid range
Basic formula: xn +/- 11
x = ploidy level; n= haploid #
