Genetics

·         The 6 × 10⁹ bp of DNA in each human diploid cell are apportioned among 46 chromosomes. Even with the highest-resolution karyotype, the average chromosome band equals about 2 × 10⁶ bp.

·         The process of introducing foreign DNA into a cell is called transformation for bacteria and transfection for eukaryotes.

·         A polymorphism is a clinically harmless DNA variation that does not affect the phenotype. In contrast, mutation refers to an infrequent, but potentially harmful, genome variation that is associated with a specific human disease.

·         Two types of DNA variation commonly result in RFLPs:

1.single-base changes in the nucleotide sequence - SNP

2. tandem repeats of DNA sequences- VNTR

·         DNA microarrays contain thousands of immobilized DNA sequences organized in an area no larger than a microscope slide. These microarrays are used to analyze a sample for the presence of gene variations or mutations (genotyping), or to determine the patterns of mRNA production (gene expression analysis), analyzing thousands of genes at the same time.

·         ELISA and Western blots can only detect HIV exposure after anti-HIV antibodies appear in the bloodstream. PCR-based testing for HIV is more useful in the first few months after exposure.

·         One of the major problems of PCR in the past was contamination from extraneous nucleic acid. There are several ways to prevent contamination and the resulting falsely positive results. They include the use of separate laboratories, hoods, gloves, and surface disinfectants. The most effective method, however, is the use of internal sterilizing agents such as uracil Nglycosyls (UNG). These agents cross-linkS extraneous DNA so that the product cannot be amplified. Primers now can be purchased from a catalogue and their sequence obtained online. Primers are easily synthesized, must be complementary to sequences on the bacterial chromosome, and when coupled to such sequences must promote replication. The specificity of PCR is a function of choosing a primer pair that is unique to the organism that you wish to detect. The PCR process is best explained by the "needle in the haystack" analogy. One needle in a haystack is difficult to find. However, if one needle becomes a million needles, then detection is easy. The same is true for nucleic acids. The amplicons (amplified nucleic acids) can be detected by a number of methods because they are so plentiful. These methods include specific staining with ethidium bromide of a gel containing these amplicons and Southern blotting of the amplicons "tags" them so that they can be seen on photographic film. Amplicons are also bound to solid phases and detected with labeled enzymes or an instrument that reads a fluorescent tag. Microscopy is not used.

·         In Autosomal Dominant (AD) disease, each of parent’s four children has a 1/2 chance of receiving the allele that causes AD and a 1/2 chance of receiving the normal allele. The probability that none of his four children received the allele for the disease thus the joint probability of four independent events, computed by the product 1/2 × 1/2 × 1/2 × 1/2 = 1/16. The probability that at least one child has received the abnormal AD Dz allele is thus 1 – 1/16 = 15/16.

·         In Autosomal Recessive Ds, For each pregnancy, the probability that the child will be affected is 1/2. Therefore, the probability that all three children will be affected is the product of the three independent events—that is, 1/2 × 1/2 × 1/2 = 1/8. The probability that all three children will be unaffected is the same. When evaluating the probability that one of the three children will be affected, it must be noted that there are three of eight possible birth orders that have one affected child (Www, wWw, wwW). For two of three children to be affected, there are also three of eight possible birth orders (WWw, WwW, wWW).

·         ( CONFUSION ) ???

Parents of children with autosomal recessive disorders are obligate carriers if nonpaternity and rare examples of uniparental disomy (inheritance of chromosomal homologues from the same parent) are excluded. Normal siblings have a 2/3 chance of being carriers because they cannot be homozygous for the abnormal allele. Grandparents have a 1/2 chance of being carriers because one or the other must have transmitted the abnormal allele to the obligate carrier parent. First cousins share a set of grandparents of whom one must be a carrier. There is a 1/2 chance for the aunt or uncle to be a carrier and a 1/4 chance for the first cousin. Half-siblings share an obligate carrier parent and have a 1/2 chance of being carriers. These calculations assume a lack of mutations (Tay-Sachs is rare) and a lack of coincidental alleles (no consanguinity)

·         Linkage disequilibrium describes an association between a particular polymorphic allele and a trait.

Many autoimmune diseases exhibit association with particular human leukocyte antigen (HLA) alleles (i.e., HLA-B27 and ankylosing spondylitis). The association is not necessarily cause and effect (e.g., when viral infections that trigger a disease preferentially infect certain HLA genotypes).

Founder effects represent a special case of genetic drift in which rare alleles are introduced into a small population by the migration of ancestors.

Genetic linkage implies physical proximity of the allele locus to the gene causing the disease. Linkage differs from allele association in that either allele A or a may be linked in a given family, depending on which allele is present together with the offending gene.

·         McKusick number allows the reader to immediately access information about the disorder using the Online Mendelian Inheritance in Man Internet site.

·         The AAT locus is located on chromosome 14 within a family of protease inhibitors called serpins. Altered AAT proteins termed M, S, or Z variants have normal inhibitory activity but are defective in their rates of secretion across the liver membrane into the blood. Lower levels of AAT protein apparently expose lung proteins to damage, causing emphysema. Heterozygotes are usually not affected, so the man may have emphysema because of cigarette smoking or other factors. Homozygous ZZ individuals may have liver disease in addition to lung disease because the abnormally secreted AAT accumulates in liver cells.

·         Fibrillin is a glycoprotein used to form a scaffold in the connective tissue filaments called microfibrils. It is distributed in the suspensory ligament for the lens of the eye, the aorta, and the bones and joints, accounting for the symptoms of Marfan's syndrome (154700).

Similar pathogenetic mechanisms occur in the osteogenesis imperfectas with multiple fractures and in the Ehlers-Danlos syndromes with skin fragility (scarring) and vascular disease due to mutations in various collagens. The mutations disrupt the alpha-helix secondary structure of collagens, which is dependent on the glycine-X-Y triplet amino acid repeats; the distorted collagen polypeptides then disrupt the collagen fibrils with symptoms dependent on its tissue distribution (2 types of fibrillin and more than 15 types of collagen are known).

·         The Prader-Willi deletion is quite small and is not usually detected by standard metaphase karyotyping. Fluorescent in situ hybridization (FISH) is the most efficient and accurate method for detecting the deletion in Prader-Willi syndrome.

·         The Ames test is a rapid and relatively inexpensive bacterial assay for determining mutagenicity of potential toxic chemicals. Since many chemical carcinogens are mutagenic, it seems obvious that damage to DNA is a central event in carcinogenesis as well as mutagenesis. Dr. Bruce Ames developed a tester strain of Salmonella that has been modified not to grow in the absence of histidine because of a mutation in one of the genes for the biosynthesis of histidine. Toxic chemicals that are mutagens are placed in the center of the plate and result in reversions of the original mutations, so that histidine is synthesized and the mutated revertants multiply in histidine-free media. Since many carcinogens are converted to active forms by metabolism in the liver, preliminary incubation with liver homogenates may precede the bacterial assay. Essentially all chemicals known as carcinogens in humans cause mutagenesis in the Ames test.

·         Template-directed RNA synthesis but not DNA synthesis occurs during the expression of oncogenes.

In contrast, template-directed DNA synthesis rather than RNA synthesis occurs during the repair of thymine dimers, the polymerase chain reaction, the functioning of the replication fork, and the growth of RNA tumor viruses.

·         The Hardy-Weinberg law predicts allele frequencies in an idealized population according to the formula p2 + 2pq + q2 = 1. Applied to cystic fibrosis, the law predicts that homozygotes (q2) have a frequency of 1 in 1600, predicting that carriers (2pq) have a frequency of 1 in 20.

·         Pedigree Patterns:

1.       AD – vertical

2.       AR-Horizontal

3.       XR-Oblique

·         Non-Mendelian inheritance mechanisms include

1.       mitochondrial inheritance (exhibiting maternal transmission),

2.       expansion of triplet repeats (exhibiting anticipation in pedigrees as in the fragile X syndrome), and

3.       genomic imprinting (exhibiting different phenotypes according to maternal or paternal origin of the aberrant genes).

·         Autosomal Dominant Diseases

Tip1 : Majority of CNSdisorders are Autosomal Dominant, the major exception being Friedrich's ataxia(AR)

Tip 2 : All Neurocutaneous syndromes/ Phacomatoses are AD except Ataxia Telengectasia.

o   MODY 1(HNF 4 alpha)

o   Familial Melanoma

o   Basal Cell Nevus Syndrome

o   Darier's Disease

o   Factor V Leiden Mutation

o   Neurofibromatosis 1 and 2

o   Von- Hippel-Lindau Syndrome

o   Sturge-Weber Syndrome

o   Tuberous Sclerosis

o   MEN 1 & 2

o   FAP

o   HNPCC / Lynch Syndrome

o   Gilbert's Syndrome

o   Alagille Syndrome

o   Peutz-Jeghers Syndrome

o   Turcot's Syndrome

o   Gardner's Syndrome

o   Juvenile Polyposis Syndrome

o   Hypertrophic Cardiomyopathy

o   Long QT Syndrome

o   Marfan Syndrome

o   Primary Pulmonary Hypertension(BMPR2 gene)

o   Adult AD Polycystic Kidney Disease

o   Familial Hypocalciuric Hypercalcemia

o   Neurohypophyseal Diabetes Insipidus

o   Familial Hyperaldosteronism

o   Bartter's Syndrome Type 5 (1,2,3 and 4 are AR)

o   Liddle's Syndrome

o   Gordon's Syndrome / Pseudo-hypoaldosteronism Type II

(Note : Liddle's - HTN with hypokalemia, Gordon's-- HTN with hyperkalemia)

o   Malignant Hyperthermia / Central Core Disease

o   Hyperkalemic Periodic paralysis

o   Familial Parkinsonism Disease

o   Spinocerbellar Ataxias

o   Dystrophia Myotonica/ Myotonic Dystrophy

o   Noonan Syndrome

o   Best Disease

o   Retinoblastoma

·         Autosomal Recessive Diseases

Note : Majority of Inborn Errors of Metabolism are Autosomal Recessive.

o  PKU

o  Albinism

o  Galactosemia

o  Canavan' s Disease

o  Refsum's Disease

o  Abetalipoproteinemia

o  Ataxia Telengectasia

o  Friedrich's Ataxia

o  Familial Mediterranean Fever

o  Alpha-1- Anti Trypsin deficiency

o  Cystic Fibrosis

o  ARPCKD

o  21-Hydroxylase deficiency

o  Bartter's Syndrome types 1,2,3 and 4 . (Type 5 is AD)(salt wasting, hypokalemia)

o  Gitelman variant of Bartter's (salt wasting, hypokalemia and HYPOMAGNESEMIA)

o  Wilson's Disease

o  Caroli's Disease

o  Hemochromatosis (HFE gene)

o  CGD / Chronic Granulomatous Disease(Don't confuse it's only 30%)

o  Chediak-Higashi Syndrome

o  Specific Granule Deficiency

o  MPO Deficiency

o  Sickle cell Anemia

o  Werner Syndrome

o  Acrodermatitis Enteropathica (Zn Deiciency)

o  Kartagener's Syndrome

o  Gyrate Atrophy

·         X-Linked Dominant Diseases

• Alport Syndome (Dominant inheritance) / Hereditary Nephritis Syndrome.
• Incontinentia Pigmenti
• Vitamin D Resistant Rickets / Hypophosphatemic Rickets

• Double check before you study the following..

• Rett syndrome
• Coffin-Lowry syndrome
• Aarsog Syndrome
• Aicardi Syndrome
• Idiopathic Hypoparathyroididsm
• OTC Deficiency

·         X-Linked Recessive Diseases

• Hemophilia A
• Hemophilia B
• G6PD Deficiency
• Fragile-X Syndrome
• Kallmann Syndrome
• Adrenoleukodystrophy
• Duchenne Muscular Dystrophy
• Becker Muscular Dystrophy
• CGD / Chronic Granulomatous Disease(Majority 70%)
• Lesch-Nyhan Syndrome
• Red Green Colour blindness
• Ocular Albinism
• Lowe's Oculo-Cerebro-Renal Syndrome
• Wiscott-Aldrich Syndrome
• SCID
• Hunter's Syndrome (MPS)
• Menke's Kinky hair disease
• Fabry's Disease

·         INCOMPLETE PENETRANCE: RB 90%, BRCA 1 70%,P53, Hereditary Hemochromatosis

·         VARIABLE EXPRESSIVITY: Hereditary Hemochromatosis, NF 1

·         PLEIOTROPHY: MFS, CF

·         LOCUS HETEROZYGOCITY: O.I. (CLO GENE, Chr 7/17)

·         ANTICIPATION: MyoD, Huntington’s, FXS

·         IMPRINTING: PWS, Angelman’s (inactivation is caused by METHYLATION)

·         Hardy Weinberg generally applied to AR or AD diseases. Not is X linked as it is applied only when there are 2 alleles inherited. YES, IT CAN BE APPLIED TO X LINKED Dz IN FEMALES.

IN XR Dz, AFFECTED MALES DIRECTLY GIVES q, not q^2.

P²+2pq+q²=1

FOR AR,

P²   is NORMAL, q²  is affected(PREVALANCE), 2pq is CARRIERS.

If PKU prevalence is given 1/10,000, then q²  is 1/10,000, so q= 1/100.

Now p=1-q = 0.99= 1

So, CARRIEER RATE is 2pq= 2*1*0.01= 1/50s

·         RECIPROCAL TRANSLOCATION: Philadelphia Chr in CML (9,22),Burkitt’s (8,14)

·         ROBERTSONIAN TRANSLOCATION: in ACROCENTICs, Down Syndrome

·         INTERSTITIAL DELETION: PWS & Angelman CHR 15

·         TERMINAL DELETION: cri du chat CHR-5

·         Genetic distances are often expressed in centiMorgans (cM). One centiMorgan is equal to a 1% recombination frequency between two loci (for example, two loci that are 10 cM apart would have a recombination frequency of 10%). Physically, 1 cM is approximately equal to 1 million base pairs of DNA (1 Mb).

To estimate the likelihood that two loci are truly linked with a specific recombination frequency, a LOD score is used. A LOD score>3 indicates linkage; a LOD score< -2 indicates no linkage.

·         Two linked loci are said to be in linkage disequilibrium if specific combinations of alleles at the loci are seen together on chromosomes more often than expected by chance.

·         The process of X-inactivation is achieved by differential methylation (a form of imprinting - p. 118) and is initiated by a gene, XIST ('X inactivation specific transcript'), which maps within the X-inactivation centre at Xq13.3.

·         Submicroscopic deletion at band 22q11 causes a spectrum of disorders ranging from DiGeorge

·         anomaly to Shprintzen syndrome.

·         Steinert myotonic dystrophy is caused by unstable trinucleotide repeats near a muscle protein kinase gene on chromosome 19; the repeats are particularly unstable during female meiosis and may cause a severe syndrome of fetal muscle weakness and joint contractures.