1. Single gene disorders - ~1500 loci known to have mutations of significance (~2%)
2. Chromosome disorders (~7/1000) - >1000 known disorders ~50% of spontaneous abortions
3. Multifactorial disorders - interaction between a number of predisposing factors such as genotype at one or more loci and environmental factors (5-60%)

• staining of metaphase chromosomes with dyes
• generates specific banding patterns for each chromosome
• Must have condensed chromosomes

acrocentric

What chromosomes?

centromere near the end of the chromosome

13,14,15,21,22

submetacentric

p arm

q arm

close to the middle but asymetrically positioned so the 2 arms are different length

short arm; long arm

1. Peripheral blood leukocytes stimulated with mitogen
2. Phytohemagglutinin (PHA) agglutinates RBCs so they can be removed with centerfuge
3. Inoculate in nutrient medium for 72h
4. Colchicine added to inhibit spindle formation
5. Hypotonic solution - cells swell: cells and chromosomes are fixed
6. Drop cells on slides - membranes break; chromosomes are attached by electrostatic forces

1. requires trypsin or heat to remove proteins
2. Giemsa staining
3. light/dark bands
4. dark bands are AT-rich (which is typically repeated DNA in the genome)
5. pattern depends on location of repetitive DNA

1. Quinacrine mustart binds
2. bright bands are AT rich - corresponding to dark G bands

• Heat treatment
• acridine orange - reverse of G bands

• centromeric region and other regions containing heterochromatin
• pentanucleotide repeat on 1,9,16,Yq

• variant in chromosome morphology or staining
• usually benign differences, reflecting defferences in the amount or type of satellite DNA

• encodes genes
• less than ~10% of human genome encodes genes
• ~50% of linear length is single copy
• Long stretches of unique DNA are rare in the genome, interspersed with repetitive DNA

• clustered repeat DNA sequences - 10-15%
• organized tandemly head to tail, comprise the satellite DNA
• pentanucleotide repeats found in heterochromatic regions of 1,9,16,Yq
• 171 base-pair unit found at centromeric region of each human chromosome

• retrotransposons
• 300 bp in length
• members of the family are related but not identical
• ~500,000 Alu family members in the genome comprising several percent of the genome
• do not code for reverse transcriptase

• long, repetitive sequences up to 6 kb in length
• 100,000 copies per genome
• can code for a reverse transposon

Function of BRCA1 gene

What percent of breast CA?

• involved in DNA repair and maintaining cell cycle control and genomic stability
• when mutated then genomic instability
• mutation followed by LOH (loss of heterozygotizity) then increase in breast and ovarian cancer

BRCA1 - 17q21

BRCA2 - 13q12

~50% of early spontaneous abortions are trisomic. Which trisomy is most common among those?

Which is most common in live borns?

Trisomy16 (8%)

Trisomy 21 (then 13 & 18)

• Hypotonia
• brachycephaly (short head)
• Flat occiput (back of the head)
• short neck w/ loose skin on nape
• flat nasal bridge
• low set, folded ears
• mouth is open showing furrowed protruding tongue
• hands are short and broad with a simian crease and fifth finger clinodactyly
• eyes have brushfield spots
• IQ 20-50
• congenital heart disease
• tracheoesophageal fistula & duodenal atresia
• 15x increase in developing leukemia
• ~50% live >50, premature senility

• Trisomy 18
• hypertonia
• prominent occiput
• receding jaw
• low set ears
• nails hypoplastic
• severe mental retardation
• short sternum
• heart defect
• specific fist clinch
• rocker bottom feet
• most die by 6 months

• Trisomy 13

• most die by 6 months; 50% in 1st month
• growth and mental retardation
• cleft lip/ palate
• congenital heart defects

FISH procedure

(fluorescence in situ hybridization of chromosomes)

Can be used for <3 Mb and interphase cells where conventional karyotyping cannot

1. DNA clone is labeled with a reporter molecule (fluorescent or capable of binding a fluorescent antibody)
2. DNA probe and target DNA are denatured.
3. The probe is mixed with the target DNA and hybridized overnight at 37C.
4. Excess probe is washed off and the slide is visualized.

Whole chromosome paint (WCP) probes

(metaphase only)

Balanced: no loss or gain of genetic material

Unbalanced: loss and/or gain

Balanced: carriers are phenotypically normal but are at risk for producing a child with an unbalanced chromosome complement

Unbalanced: usually phenotypically abnormal and mentally retarded

inv

Paracentric vs. Pericentric

• Inversion
• results from 2 breaks in the same chromosome which makes a 180 degree turn

• deletion
• interstitial (2 breaks)
• terminal (1 break) - usually de novo; size of deletion and function of gene determine the phenotype

ins

direct vs. inverted

• insertion
• removal and insertion of a chromosomal segment to a different site on the same or different chromosome

• exchange of chromosomal material between 2 or more non-homologous chromosomes
• each derivative (der) chromosome is named for the chromosome from which its centromere originated

• ring
• formed when 2 ends of a chromosome break and join, forming a ring
• rings are very unstable and may be lost during cell division

• duplication
• an additional copy of a chromosome segment, resulting in a partial trisomy. Tandem array with the original segment - direct or inverted.
• originate by unequal crossing over or by abnormal segregation during meiosis
• less harmful than deletions
• chromosome breaks that generate the duplication may disrupt important genes, which can lead to some phenotypic abnormalities

i

2 methods

• isochromosome
• duplicated arm and loss of the other arm (usually loss of p)
• occur in a somatic cell or germ cell

Robertsonian translocations

Phenotypical effect

Percentage of Down Syndrome

Fusion of the centromere region of 2 acrocentric chromosomes with loss of the short arm

carriers are phenotypically normal; at increased risk of miscarriages and have abnormal live born children

<5%

1. Trisomy 21 (95%)
2. Robertsonian translocation (4%)
3. q21q21 translocation (originate as isochromosome)
4. Mosaic Down Syndrome (somatic mosaicism)
5. Partial Trisomy (very rare)

• associated with specific and relatively large deletions in autosomal chromosomes
• or very small deletions

• crying infants sound like a mewing cat
• hypertelorism; epicanthal folds (a vertical fold of skin of either side of the nose, retrognathia (position of the jaw behind the frontal plane of the forehead)
• deletion in 5p; ~1% of institutionalized mentally retarded
• 15% result from unbalanced product of a balanced translocation in a carrier parent
• hemizygous

• small deletions
• segmental aneusomy NOT PARTIAL MONOSOMY
• phenotype is attributable to haploinsufficiency of multiple, contiguous genes within the deleted region

DiGeorge Syndrome

velocardiofacial syndrome

• 1:2000-4000 live births
• autosomal dominant - (d 22q11)
• variable expressivity
• ~3000 bp deletion
• craniofacial anomalies; mental retardation; heart defects; tetrology of fallot; pulmonary atresia (40% no pulmonary valve)

• paternal deletion of 15q11-13
• Infantile feeding difficulties; hyperphagia and obesity; hypotonia; cognitive impairment; small hands and feet; short stature; mental retardation; dysmorphism

• maternal deletion of 15q11-13
• unusual facial appearance; short stature; severe mental retardation; seizures; spasticity; "happy puppet" - distinctive laugh always laughing
• 70% caused by deletion; 30% UPD uniparental disomy for PWS

Uniparental Disomy (UPD)

What is this an example of?

What percents of PWS and AS?

Child has 2 copies of the chromosome (15 in PW and AS) from only one parent. Example of genomic imprinting

30% of PW syndrome; 5% of AS

• normal process caused by alterations in chromatin that occur in the germline of one parent, but not the other, at characteristic locations in the genome.

• abnormal pregnancy, the placenta is converted into a mass of tissue resembling a bunch of grapes called a hydatid cyst.
• abnormal growth of chorionic villi, in which the epithelium proliferates and the stroma undergoes cystic cavitation - called a mole (can be complete or partial depending on parental chromosomal contribution.
• caused by paternal diploidy or triploidy

• Benign tumors that arise from 46, XX cells containing only maternal chromosomes