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Human genetics

PedigreeA graphical family tree using standardized symbols.
Germ CellConstituting the germline, germ cells differentiate into sperm or eggs and pass genetic information to progeny.
Somatic CellAny cell that is not a germ cell; genetic information within a somatic cell will not pass on to progeny.
Genea section of DNA (xsm) that codes for a product.
LocusThe location of a gene on a chromosome.
AlleleA version of a gene. For example, there is a hair color gene. An allele of that gene might encode brown hair.
Wild-TypeThe most common form(s) of an allele in the overall population.
MutationAny change in the nucleotide sequence or arrangement of DNA.
MutantArising from mutation, a mutant (aka variant) allele is any other than the wild-type allele(s).
PolymorphismIf there is more than one common allele for a gene -- such as with hair color -- then that gene is polymorphic.
Rare VariantIf an allele is present in less than 1% of the population, it is a rare variant (as opposed to a polymorphic allele).
HaplotypeThe different alleles possible at a given locus.
CentromereA centromere (abbreviated cen is the center of a chromosome, where sister chromatids meet.
GenotypeAn individual's set of alleles.
PhenotypeThe phenotype (aka trait) is the manifestation of a genotype, ranging from retardation to hair color. Genetic variation (allelic heterogeneity, locus heterogeneity and gene modifiers) muddles the genotype-phenotype correlation.
Qualitative TraitA trait that is either present or not, such as trisomy 21.
Quantitative TraitA trait that is measured, such as height, body mass index or intelligence.
Single-Gene TraitA trait that is mostly determined by the alleles at a single locus.
Polygenic TraitAka multigenic, any trait (or disease) that is controlled by several genes.
Allelic HeterogeneityAllelic heterogeneity is different mutations in the same gene resulting in the same disease, even if of different severity. An example is cystic fibrosis. ther diseases, like sickle cell disease, show little or no allelic heterogeneity (since a single mutation causes it).
Locus HeterogeneityDifferent genetic diseases causing the same phenotype. An example is retinitis pigmentosa.
Phenotypic HeterogneityDifferent mutations in the same gene can cause very different diseases. A deletion in the RET gene causes Hirchsprung Disease, characterized by severe constipation; other mutations in the RET gene result in thyroid and adrenal cancer; another set of mutations causes both Hirschsprung disease and cancer.
Inbreeding Coefficient (F)
HomozygousHaving the same alleles on each homologous chromosomes.
HeterozygousHaving different alleles on each homologous chromosome. A compound heterozygote carries no normal alleles (only mutant alleles) for a particular gene.
HemizygousA gene with only one copy (and thus only one allele) normally present; for example, a Y gene is hemizygous).
Dominant AlleleIn a heterozygote, only the dominant allele is expressed.
RecessiveIn a heterozygote, the recessive allele is not expressed.
MultifactorialAka complex, any disease caused by complex genetic (gene-gene or polygenic) and environmental (gene-environment) interactions, and not following a Mendellian pattern.
AutosomalNot pertaining to a sex chromosome (an autosome being any chromosome not a sex chromosome).
PenetranceThe likelihood that a disease genotype leads to disease phenotype.
ExpressivityEither constant or variable, expressivity describes disease severity among individuals with the same genotype.
ConcordanceWhen two family members share a disease, the two individuals are concordant for the disease.
DiscordanceWhen two family members do not share a disease, the two individuals are disconcordant for the disease.
GenocopyA concordant relative has a genocopy (aka phenocopy) if they express the disease for different genetic reasons.
Balanced TranslocationNot always detrimental. Same information, just different places. But if the break causes a fusion protein (Philadelphia chromosome) then it is inappropriately activated).
DNA Mismatch RepairDNA Mismatch Repair Genes are needed for repairing DNA. Familial Adenomatous Polyposis (FAP)—germline mutation in APC tumor suppressor gene (Chr 5), followed by accumulation of additional mutations. Hereditary Non-polyposis Colorectal Cancer (HNPCC)—linked to multiple loci other than Chr 5. Not associated with LOH at these loci, but rather instability of repeated sequences.
TelomeraseSomatic cells have a finite replicative potential, after which point they reach a crisis and senesce. With each cell division, chromosome ends (telomeres) are shortened due to inability to replicate ends. 90% of tumors reactivate telomerase. It is required for genome stability, but the genome grows increasingly unstable once senescence is reached and genomes are usually unstable in the oft-oncogenic Telomerase-activated somatic cells (usually only activated for gametogenesis).
Deletion MappingDeletions at various points along gene; locate which deletions leads to phenotype. Critical region will be consistent in all deletions which lead to phenotype.
MicrodeletionsSmall chromosomal deletions which require FISH for visualization. An example of a microdeletion is the family of 22q microdeletions, leading to Velocardiofacial and DiGeorge syndromes characterized by CATCH 22 (cardiac defect, abnormal facies, thymic hypoplasia, cleft palate, hypocalcemia, 22q11 deletions).
William's SyndromeDeletion on chromosomal 7q11.3, involving the elastin locus and other genes; phenotype can reflect variety of severity.
NeurofibromatosisAn autosomal dominant disease involving the NF1 disease -- a disease with 100% penetrance
Prenatal DiagnosticsCVS @ 11 weeks; early amniocentesis @ 12-15 weeks; routine amniocentesis @ 16-20 weeks.
Linkage AnalysisFrequently not possible for complex traits, constructs a transmission model to explain inheritance of a disease in a pedigree.
Allele-SharingAllele sharing methods involve testing whether affected relatives inherit a region identical-by-descent more often than expected under random Mendellian segregation, and makes no assumptions about inheritance mode. Just determines if certain alleles are more present in affected individuals. An exampel is sib-pair analysis.
Association StudyIs a given allele more present in affected than non-affected individuals? Involves whole populations, not just cosegregation in a family. For example, certain HLA alleles are very present in certain disease phenotypes.
GWAGenome-wide association studies testing at thousands or millions of alleles for disease association.
SNPsSNPs involed with disease are identified via tables of various sequences and locating which regions are consistently changed in diseased individuals but not wild-type individuals.
Rare VariantsMassive parallel sequencing allows identification of rare variations contributing to rare and common disorders. Randomly fragment DNA and ligate adapters to both ends. Bind single-stranded fragments randomly to the inside surface of flow cell surface. DNA fragments will form "U-shaped" bridges, with both adapters bound to the well surface. Add unlabeled nucleotides and enzymes to initiate amplification of these regions. Fragments become double-stranded, with the new strand being slightly shorter at both ends than the bridge. Repeating this will generate severa million dense clusters of dsDNA that is no longer bridged in each channel of the flow cell, then determine first base of all clusters using nucleotides which are each labeled differently so you can distinguish G, C, T and A -- result is an image with lots fo differently-colored dots. Then remove that nucleotide, and repeat until you have sequenced the fragments.
VariationGenotyping is identification of genetic difference, best way to locate rare mutation is sequencing. Genetic variations present in populations arise as a result of mutations. Dominant lethal variations are rare. Polymorphisms are common variations (1% or more) and probaly arose early in evolution. Single nucleotide polymorphisms (SNPs). Polymorphisms provie genetic markers that identify chromosomal regions segregating (linkage analysis). Restriction fragmnet length polymorphisms (RFLPs) identify DNA variations also. Tandem repeat sequence polymorphisms arise by replication slippage and are useful for this. PCR amplifies short tandem repeats and is most useful for linkage analysis. Genome wide association uses tousnads/millions of SNPs to identify common variations contributing to complex genetic traits such as genes for heart disease, diabetes or schizophrenia. Polymorphisms in the human population tend to be old.Polymorphism useful for identity, paternity and forensics testing. Lots o diffrent polymorphisms for high specificity. As well as migrations since migrated subpopulation within same species exlcusively have some alleles, and for history of genes (lactase persistience arose indepdently in African and Europe). Polymorphisms/mutations farm from exonic sequence an influence gene expression. Polymrphisms are RFLP, VNTR, STR, SNP.
DNA FingerprintingPaternity testing, establishing twin zygosity, determining bone marrow transplant engraftment, identifying mislabeled pathology species (major!), pedigree analysis of animals and animal products, and establishing identity of criminals. CODIX is an FBI-administered DNA index.
Mutationsare either deletions (Cri Du Chat), duplications, insertions or translocations. Biochemical genetics looks at one mutated gene at a time to establish roles .
Quinacrine BandingBright q-bands are AT rch, late replication and relatively gene poor
FISHLabeling, denaturing, hybridiziation and visualization. There are gene-specific, centromeric, telomeric and chromosome-painting probes. Interphase FISH can locate extra centromeres, leading to easy identification of trisomies. Interphase gene-specific FISH would be good for diagnosing diseases, as it would just tell you if a disease allele is present. Metaphase FISH is useful for identifying small chromosomal deletions and translocations.
Competitive Genome HybridizationComparative genomic hybridization (CGH), aka Chromosomal Microarray Analysis (CMA), is a cytogenetic method for analyzing small mutations (like deletion) and for copy number changes (duplications or losses of a gene). It is frequently used for tumors.
SKYSpectral karyotyping is a molecular cytogenetic technique used to simultaneously visualize all the pairs of chromosomes in an organism in different colors. Fluorescently-labeled probes for each chromosome are made by labeling chromosome-specific DNA with different fluorophores. Because there are a limited number of spectrally-distinct fluorophores, a combinatorial labeling method is used to generate many different colors. Spectral differences generated by combinatorial labeling are captured and analyzed by using an interferometer attached to a fluorescence microscope. Image processing software then assigns a pseudo color to each spectrally different combination, allowing the visualization of the individually colored chromosomes. This technique is used to identify structural chromosome aberrations in cancer cells and other disease conditions when Giemsa banding or other techniques are not accurate enough.
Chormosome abnormalitiesChormosome abnormalities are somatic/acquired, numerical/structural, balanced/unbalanced.
Structural RearrangementsPericentric or pracentric inversion; robertsonian or reciprocal translcoations. When balanced, leads to normal phenotype but problems in meiosis. Translocation, two chromosomes exchange parts. Reciprocal translocation is when two non-homologus chromosomes exchange DNA, requires two breaks. Robertsonian can be balanced or unbalanced.
Philadelphia Chromosome
Contiguous Gene Syndromes
PolyploidyTypically via non-disjunction, where meiosis leads to two diploid cells and then four haploid cells. Howver, non-disjunction occurs in the second meiotic division and causes on cell to lack a chromosome and the other to be diploid still, with two normal haploid cells. Example is kilnefelter, 47,xxy. Monosomy (like Turner Syndrome, 45,x) is
Copy Number VariantsCNVs are larger insertions/deletions (Charcot Marie Tooth syndrome is an example).
Non-coding RNAMost of human genome encodes RNA, but only 2% encodes protein. Non-protein-coding RNA genes may account for transfer RNA (tRNA), ribosomal RNA (rRNA), small nucleolar RNA (snoRNA) for RNA modification and processing, small nuclear RNA (snRNA) for mRNA splicing, miRNA that regulations mRNA transcription levels), antisenseRNA that inhibits translation of complementary mRNA.
Human vs Others

Protein coding changes alone are unlikely to determine human-chimp differences. Sequence differences in non-coding DNA that influences expression levels are likely to be critical.Which species comparison is most useful?

• Human-mouse comparisons (80 Myr)
• Human-fish comparisons (400 Myr)
• Human-chicken comparisons (300 Myr)
• Human-primate comparisons
• Human-human comparisons

Allele FrequencyFor two-allele genes, AA=p2, AB=2pq and BB=q2. For genes with multiple alleles, just keep expanding... AA=p2, BB=q2, CC=r2, AB=2pq, AC=2pr, BC = 2qr.
Some alleles are deleterious in a homozygous but provide a heterozygous advantage, like sickle cell anemia. Dominant alleles with fitness <1 disappear after several generations; recessive allles with fitness <1 remain, just less frequently than other alleles.
MicrosatellitesMicrosatellites are small repeats like GAGAGA which expands or contracts due to DNAP slippage. Lots of bands is indicative of poor DNA matching or mismatch repair.
People with familial adenomatous polyposis have mutantions in AC tumor suppressor gene... lots of polyps by age 15, but then if one polyp mutates then TUMOR! hereditoary non... what?
Genomic Imprinting

DNA methylation may mediate transcriptional repression by histone deacetylation and histone methylation. The methylation imprint established in early development is maintained by a “maintenance methylase” that recognizes hemimethylated DNA and methylates the CpG on the other strand. Methylation occurs most often in occurs most often in cytosines of CpG islands; these islands are relatively rich in CpG dinucleotides and are often associated with genes. Imprinted genes have CpG islands which are methylated differently on the maternal and paternal alleles.

During gametogenesis, the old imprint must be erased and a new sex-specific imprint must be established. Different genes can be active or silenced on the same parental homologue. Beckwith-Wiedeman syndrome arises when a patient has both Chromosome 11's from the same parent -- this leads to bilallelic expression of IGF2 (growth factor gene) and biallelic silencing of H19 (tumor suppressor gene).

Hypermethylation leads to chromatin condensation and gene silencing. Not all imprinted genes are hypermethylated at their promoters; some are hypermethylated at intergenic control regions called imprinting centers that control imprinted gene cluster (called enhancer blocking). Identical deletions of Chr 15 cause PWS when maternal UPD (silencing of matneral genes) inherited or AS when paternal UPD (paternal alleles silenced). So far all PWS cases are new due to sterility of patients; some AS cases are familial, with unaffected fathers passing a mutant gene to half their offspring of tiether sex. If a son passes the mutant on it will not show. If a daughter does then half her kids will have AS, leading to its appearance in multiple progeny over mutliple genrations.

Euchromatic Genes Active -regulated- Inactive (silenced) –Normal gene regulation @ development –Abnormal (cancers) –Normal parent specific germ line silencing (imprinting)
Aneuoploidy
Uniparental DisomyBoth chromosomes are from one parent -- isodisomy if they are identical, heterodisomy if not. Examples are Prader-Willi, Angelman, Beckwith-Wiedemann, .
HemoglobinOyxgen carrier in vertebrate red blood cells. Tetramer, with 2 identical α chains and 2 identical β chain. Each globin chain covalently linked to a heme group, an iron-containing pigment binding oxygen The common adult hemoglobin is HbA, written α2β2. Classic model for proteins and mutations. Mutations resulting in amino acid substitution lead to a difference in the charge of the protein, are co-dominant as electrophoreti phenotypes and easily seen in heterozygotes. Patients without HbA are anemic.
Electrophoretic MobilityUses amino acid changes leading to protein charge differences to identify mutants. Different Hbs can be separated from each other using electrophoretic mobiliity.
Sickel CellAutosomal recessive. Heterozygote (only!) advantge resistance to malaria. HbS is due to a single amino acid substitution in the β globin chain. Fiber polymerization is new protein property of HbS
Hb HammersmithReduced O2 binding by heme group.
Hb KempseyBinds but fails to release O2
Compound heterozygotesDifferent mutations in same gene in a patient have disease similar to homozygosity for mutant allele. For example, BetaS/BetaHammersmith is affected.
X Chrsm Inactivation

Explains why monozygotic twins might have different phenotypes, with one child having an X-linked disorder and the other child not. In a normal female, only one of the two X chromosomes present is genetically active, the other being inactivated. X-inactivation occurs early in development. The inactive X can be either maternal or paternal in origin; the choice is random. X inactivation is irreversible in somatic cells, such that the inactive X in a particular cell remains inactive in all descendants of that cell. In most mammals, one X in females is inactivated. Alternatives are for one X in male hypertranscribes, two X's in female hypotranscribe or the apternal X chromosome is inactive. In the early zygote in/activation, all descendant cells have inactivation or in alte blastocyst it is random and their is mosaicism.

Properties of the inactive X chromosome:
  1. Most (but not all) genes are inactivated at the transcriptional level.
  2. Heterochromatic
  3. Late replicating
  4. Highly methylated at CpG islands
  5. Histone hypoacetylation
  6. Enrichment for the variant histone macroH2A

Epigenetic regulation is stable transmission of gene expression to daughter cells in absence of change in DNA content or sequence. This is due to chromatin structure, DNA mod or both. Methylation imprint established in early dvelopment is maintined by maintenance methylase that recognizes hemi(one strand)methylated DNA and methylates CpG on other strand. CpG dinucleotides are targets for DNA methylation, and methlyated CpG are targets for specific binding by proteins like MeCP2. MeCP2 recruits histone deacetylases that remove acetyl groups from histone tail.

X inactivation involves a recognition step (referred to as counting counting) in which the number of X chr in a cells is counted relative to cell ploidy so that only a single X chr is functional per diploid adult cell.

  1. Xist is initially expressed as an unstable transcript from both X chrs in undifferentiated ES cells and is perhaps prevented from coating the X chr by a blocking factor.
  2. After counting and choice, Xist expression increases on the Xi and is repressed on the Xa. The coating of the Xi by Xist may involve long interspersed nuclear elements (L1 repeats).
  3. Coating of the Xi establishes the inactive state. The coated Xi begins to replicate late in the S phase of the cell cycle (asynchronous replication), a hallmark of the Barr body (Xi) in adult cells.
  4. MacroH2A recruitment and H3/H4 hypoacetylation stabilize the heterochromatic state. Widespread methylation of promoters further ensures faithful transmission of this state to all daughter cells. At this point Xist expression is not required although it is retained.
der(a)/der(x)Abnormal X chromosomes are usually inactivated, due to selection since the abnormal cells are fault. If there is an X;autosome translocation, the normal X chromosome is preferentially inactivated so that there is not ianctivation of the autosome. However, the progeny are unbalanced and carry the X inactivation center leading to ivnariable inactivation of athe chromosome with the normal X always active. Se page 103.
XicAn 80 kb region of the X-chromosome that is required for X-inactivation to occur. It is responsible for initiating X-inactivation in cis: An X-chromosome that carries Xic can become inactivated, whereas one in which Xic is missing cannot. The Xic is also responsible for “counting”, whereby a single X is kept active and all other Xic carrying chromosomes are inactivated. First gene identified in Xic recgion was X inactive specific transcript (Xist) --- this gene is expressed exclsuively from inactive X chromosomes, procuing a spliced noncodiing trancript that is the primary signal for spreading inactive state along chromosome. Xist recruits histone deacetlyases and a unique histone called macroH2A which causes chromatin condensation and gene silencing. A second Xic gene is Tsix (reverse of Xist) which encoded a noncoding RNA that controls Xist in cis and is complementary to Xist. How might Tsix inhibit Xist expression???
Xic Crosstalk

The choice of Xa and Xi always occurs in a mutually exclusive manner. What mechanism mediates the crosstalk?Hypothesis: Choice is mediated by a physical interaction of X-chromosomes (chromosome kissing).

Experiment: Measure distance between Xic regions during ES cell differentiation. During XI establishment the X chromosomes become very near and then separate. This can be done by formaldehyde induced crosslinks of near DNAs, followed by digestion, ligation of the two DNA segments and then detect ligation product by quantitative PCR.

Barr BodyThe number of Barr bodies is thus one less than the number of X-chromosomes. The condensed, single X-chromosome, appearing as a densely staining mass, that is found in the nuclei of somatic cells of female mammals. Is derived from one of the two X-chromosomes which becomes inactivated. Barr bodies are commonly referred to as sex chromatin. The human abnormalities called Kleinefelter's syndrome and Turner's syndrome both result from an unnatural presence or absence of a Barr body. In the case of the former, the male possesses a Barr body that it would normally not have, and in the latter case the Barr body is absent. There is logically lots of Xist RNA in in individuals with inactivated X chromosomes (none in normal 46,XY males).
Turner SyndromeWhy do 45,X females (only one X chromosome) have such severe phenotypes?
Werner SyndromeVery rare autosomal recessive progeria.
Alzheimer'sAmyloid Precursor Protein (APP) leads to amyloid plaques and memory deficits -- also, presenilin 1 and apolipoprotein E4 enhance the Alzheimer's phenotype.
Angelman/PWSGenetic info only from father in Angelman; only from mother in PWS. Involves Chromosome 15. 15q11-q13 is a tipoff of these disorders.
Mouse GeneticsInbred strains: unlimited identical twins with a unique set of alleles useful for research purposes. Spontaneous mutations, however, influence gene expression, structure or presence. Transgenics is the random insertion of engineered genes to produce enhanced expression, and can be inducible. Targeted mutations alter endogenous genes in a controlled manner to create null or mutant alleles. Induced mutations are random chemically induced point mutations; gene-trap insertions inactivate genes.
Transgenic MiceThis adds a new gene to the normal genes. DNA construct is microinjected into pronuclei of fertilized eggs; these eggs are transferred to pseudopregnant females. 30% of surviving progeny will have the microinjected DNA heritably integrated into their genome. Transgenic animals have variability transgene expression due to construct, promoter, site of integration and number of copies inserted. This is usually measured using mRNA expression.
Regulated TransgeneTransgenes can be expressed in a reversible or inducible manner. There is a bacterial tetracycline repressor protein which binds strongly to tetracyclne operator sequences, but is displaced in presence of tetracycline, its derivativees or its analogs. The repressor protein is then converted into an activator by fusion with the transcriptional activation domain from a viral protein.
Gene-TargetingGene-targeting allows creation of knockouts and insertion of new genes.
ES CellsES cells are usually strain 129 and recipient blastocyst is C57BL/6, leading to possible observed phenotype due to the targeted gene being expressed on different genetic backgrounds.
Cre/LoxThe Cre/Lox system is used for making conditional knockouts. The essential exon is flanked by loxP sites (locus of X-ing over) which are 34 base pair sites where Cre (causes recombination) takes effect -- Floxed regions (flanked by loxP sites) are excised. However, mating two engineered mice -- one who carries a Floxed region, and a transgenic mouse expressing Cre in specific tissues -- allows genes to be knocked out in certain tissues only. Also, Cre can be attached to a promoter activated by specific chemicals that can be added at desired times to the animal's diet.
Knock-InA targeting vector can be gene-targeting to recombine and insert a new gene and a Floxed neomycin gene into ES cells. These ES cells are then transfected with CMV expressing a Cre gene. This leads to a targeted locus without neomycin, and these ES cells are injected into blastocysts.
Population geneticsPopulation genetics describes the inheritance of traits in populations over time. A population is defined as members of a species that mate and reproduce with one another. The gene pool is the sum total of genetic information in a population. Drift is a minor change in the genome that results in a significant change in an organism. Shift is a major change in the genome that results in a drastic change in an organism.

Abbreviations

FISHFluorescent in situ hybridization (aka ish).
pShort arm of a chromosome
qLong arm of a chromosome
marMarker chromosome
rRing chromosome
iIsochromosome
derDerivative chromosome
dicDicentric chromosome
cenCentromere
terTelomere, or at the end
delDeletion
dupDuplication
fraFragile site
insInsertion
invInversion
tTranslocation
rcpReciprocal translocation
robRobertsonian translocation
+Gain or addition
-Loss or omission
:Breakage
::Breakage and joining
/Mosaic
arr cghArray competitive genome hybridization

Studies

Abbreviations derived from Nussbaum, McInnes & Willard: Genetics in Medicine, 7th ed. Philadelphia, Saunders, 2007. (pg 66)

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