GU BMS141 Lecture 1 & 2 Fall 2024 PDF

F A C U L T Y O F M E D I C I N E F A L L 2 0 2 4  BMS141 # Lecture 1 & 2 # Genetics Chromosomes and chromosomal Aberrations Ola Ali Khalifa, MD, PhD Professor and Consultant of Medical Genetics Medical Biochemistry & Mo...

F A C U L T Y O F M E D I C I N E F A L L 2 0 2 4  BMS141 # Lecture 1 & 2 # Genetics Chromosomes and chromosomal Aberrations Ola Ali Khalifa, MD, PhD Professor and Consultant of Medical Genetics Medical Biochemistry & Molecular Biology Section Dept. of Basic Medical Sciences 2 Intended Learning Outcomes By the end of this Lecture, you should be able to: ▪ Define chromosome and describe its structure ▪ Differentiate between numerical and structural chromosomal abnormalities ▪ Identify different techniques of studying chromosomes What are chromosomes? Chromosomes are thread like structures located in the cell nucleus. Chroma (=color) and soma (=body). 4  Chromosome Structure The centromere divides the chromosomes into short and long arms ,designated p and q. Morphologically chromosomes are classified according to the position of the centromere. Metacentric submetacentric Acrocentric 5  Chromosome Number ❑In humans, normal cell nucleus contains 46 chromosomes, made up of 22 pairs of autosomes and a single pair of sex chromosomes (XX and XY) ❑Human female have two X chromosomes (46, XX), while males have on X and one Y chromosome (46, XY) ❑One member of each of these pairs is derived from each parents. 6 Normal male 46, XY  Normal female Normal female 46, XX 46, XX Terminology CONT’D Normal numbers of chromosomes in germ cells (ova or sperm ) is 23= haploid = 1n Normal numbers of chromosomes in somatic cells is 46 (23 pairs= diploid= 2n) 9 Terminology CONT’D Polyploid: Complete set (s) of extra chromosome e.g {triploid (3n=69), tetraploid (4n=92)} 10 Terminology CONT’D 11  Terminology CONT’D Aneuploidy: loss/gain of single chromosome Monosomy: Loss of one chromosome (45) Trisomy: Gain of one chromosome (47) 12 Chromosomal Aberrations Chromosomal Abnormalities of chromosomes may aberrations be either numerical or structural and may involve one or more autosomes, sex chromosomes, or both Numerical Structural Deletion Aneuploidy Polyploidy Duplication Translocation Monosomy Trisomy Triploiody Tetraploidy (45) (47) (69) (92) 13  Aneuploidy Most common and clinically significant type of human chromosome disorders. Most commonly due to meiotic nondisjunction. Most aneuploidy patients have either trisomy or monosomy. 14 Nondisjunction  Trisomy Gain of one chromosome Whole chromosome trisomies are viable for chromosomes 13, 18, 21, X, and Y. The most common type of trisomy in live born infants is trisomy 21 (47, XX or XY, +21) 16 47, XX,+21 Down Syndrome Diagnosed at birth or shortly thereafter by characteristic dysmorphic features 17 Genetic Causes of Down Syndrome  Trisomies Examples ❖ The most common numerical chromosomal anomalies found in humans Trisomy 21 or Down Syndrome Trisomy 18 or Edward syndrome Trisomy 13 or Patau syndrome 19  Monosomy The presence of only one member of a chromosome pair. All complete autosomal monosomies appear to be lethal early in development Sex chromosomal monosomy, however, can be viable e.g. Turner syndrome (45, X) 20  Turner Syndrome 45,X A girl with turner syndrome with characteristic short stature and neck Chromosomal Aberrations Chromosomal aberrations Numerical Structural Deletion Aneuploidy Polyploidy Duplication Translocation Monosomy Trisomy Triploidy Tetraploidy (45) (47) (69) (92) 22  Structural Chromosomal aberrations Many different types of structural chromosomal anomalies exist, including deletion, duplication, ring chromosome, isochromosome and translocation. 23 Deletion A portion of the chromosome is missing or deleted. Known disorders in humans include Wolf-Hirschhorn syndrome , and Cri du Chat syndrome. Duplication A portion of the chromosome is duplicated, resulting in an extra genetic material. Known human disorders include Charcot-Marie-Tooth disease Ring A portion of a chromosome has broken off and formed a circle or ring. This can happen with or without loss of genetic material. Isochromosome Formed by the mirror image copy of a chromosome segment including the centromere.  Translocation A portion of one chromosome is transferred to another chromosome. There are two main types of translocations. Robertsonian Translocation An entire chromosome has attached to another at the centromere. In humans these only occur with acrocentric chromosomes 13, 14, 15, 21, and 22. Reciprocal Translocation Segments from two different chromosomes have been exchanged Cytogenetic Diagnostic Techniques 33  Background Clinical cytogenetics is the study of chromosomes, their structure, and their inheritance, as applied to the practice of medicine. Today, chromosome analysis with increasing resolution and precision at both the cytologic and genomic levels is an important diagnostic procedure in numerous areas of clinical medicine. Current genome analyses, including chromosomal microarrays and whole genome sequencing (WGS), represent impressive improvements in capacity and resolution. 34 When do we ask for cytogenetic analysis? Clinical indications for cytogenetic analysis: Problems of early growth and development. Stillbirth and neonatal death. Fertility problems. Family history of chromosomal abnormalities. Pregnancy in women with advanced age. 35 Conventional Karyotype Photomicrograph of an individual chromosome arranged in a standard manner. Any tissue with living nucleated cells, which undergo division can be used for studying human chromosomes (circulating lymphocytes, amniocytes, and bone marrow) 36  Karyotype Photomicrograph of an individual chromosome arranged in a standard manner 37  Karyotype Chromosome preparation 38 Normal male 46, XY What abnormalities can be detected with conventional karyotyping? Whole chromosome aneuploidy (trisomy) Large structural chromosome anomalies 40  Conventional karyotyping CONT’D -G banding at 400 to 550 band stage of resolution -Arrest cell division during metaphase -Detects large abnormalities of greater than 5-10MB anywhere in the genome. Whole chromosome aneuploidy (trisomy) Large structural chromosome anomalies What about deletions smaller than what can be detected by conventional karyotype?? High resolution banding technique Division stopped at an early stage of mitosis (prophase or prometaphase). The chromosomes are still in a relatively uncondensed state. Detects subtle chromosomal abnormalities. More detailed banding technique (up to 850 bands or even more in a haploid set). 42 What is the advantage of high-resolution banding? Detects subtle chromosomal abnormalities that cannot be detected by conventional karyotyping.. More detailed banding technique. 43 Fluorescence In Situ Hybridization (FISH) 44  What is FISH? It is a targeted approach to determine whether specific DNA sequence as visualized with a fluorescent probe, is present within a specific chromosome prepared on a microscope slide. This confluence of genomic and cytogenetic approach is called molecular cytogenetics. 46  FISH: Background In FISH, a DNA probe is stained with a special fluorescent stain specific for either individual chromosome (paint) or very small or minute chromosomal regions (microdeletions). FISH analysis can be performed on metaphase cells or on interphase nuclei. Its use is limited to targeting a specific genomic region based on a clinical diagnosis or suspicion. 47 Advantages of FISH technique over conventional karyotype analysis: Conventional karyotype detects only large aneuploidies or rearrangements while FISH technique can detect aneuploidies or rearrangements of any size. Results of FISH technique can be obtained in a short time compared to conventional karyotyping. FISH technology provides much higher resolution and specificity than G-banded chromosome analysis. 48 Fluorescence In Situ Hybridization (FISH) Interphase FISH Metaphase FISH 49 Chromosomal Microarray (CMA) 50  CMA: Introduction CMA has replaced G-banded karyotype as the frontline diagnostic test to detect genome-wide copy number imbalances at higher resolution extending the concept of targeted FISH analysis to test the entire genome. CMA simultaneously queries the whole genome on a glass slide containing regularly spaced DNA probes that represent loci across the entire genome. 51  CMA: Introduction CON'T This technology detects relative copy number gains and losses in a genome-wide manner by hybridizing equal amounts of control and subject DNA to the DNA probes and calculating the ratio of each DNA sample hybridized to each probe. Microarray probes showing equal ratio of subject and control DNA indicate normal copy number at the respective genomic loci. An excess of subject DNA indicates copy number gain, whereas underrepresentation of subject DNA indicates copy number loss at the genomic loci represented by the microarray probes 52  CMA: Advantage Microarrays have been used successfully to identify chromosome and genome abnormalities in children with unexplained developmental delay, intellectual disability, or birth defects, revealing a number of pathogenic genomic alterations that were not detectable by conventional G-banding. This technique has the potential to provide a much more sensitive , high-resolution assessment of the genome. 53  CMA: Disadvantage CMA measure only the relative copy number of DNA sequences but not whether they have been translocated or rearranged from their normal position(s) in the genome. Further characterization of copy number variants (CNVs) by karyotyping or FISH is important to determine the nature of an abnormality and thus its risk for recurrence for other family members. 54 Chromosomal Microarray Spectrum of resolution in chromosome and genome analysis 57