Week 4 2024 Structural Chromosome Abnormalities PDF

Structural Chromosome Alterations Introduction Infinite number of ways chromosomes can configure themselves from the normal 23 pair arrangement Not all result in adverse effects, some are considered normal variants (pericentric inversion chromosome 9 heterochromatin) Types – Deletions (del), Dicentr...

Structural Chromosome Alterations Introduction Infinite number of ways chromosomes can configure themselves from the normal 23 pair arrangement Not all result in adverse effects, some are considered normal variants (pericentric inversion chromosome 9 heterochromatin) Types – Deletions (del), Dicentrics (dic), Duplications (dup), Inversions (inv), Isochromosomes (i), Rings (r), Translocations (t) Mechanism of formation The exchange of genetic material between sister chromatids and homologous chromosomes is a normal occurrence in somatic and germ cells – When these exchanges occur between non-allelic chromosomal regions structural rearrangements result (Non-allelic homologous recombination; NAHR) Chromosome breakage – Some areas are more prone then others – Breaks can occur during DNA recombination, replication and repair associated processes Risk factors Low copy repeats (LCR) High copy repeats (HCR) DNA hotspots Low copy repeats (LCR) Also known as ‘segmental duplications’ Evidence for recurrent chromosomal rearrangements that form secondary to LCRmediated non-allelic recombination Implicated in >25 recurrent genomic disorders. LCRs that serve as substrates for these recombination events range in size from 1400 kb and share >90% sequence identity Most frequent LCR recombinations occur between LCRs >10Kb and have 97% homology Seem to appear preferentially within pericentromeric chromosomal regions Direct LCR located on the same chromosome (intrachromosomal) can mediate both duplications and deletions Recombination in the reverse direction can cause inversions Non-allelic recombination events involving LCRs located on different chromosomes would result in translocations One of the most frequent LCR mediated aberrations is DiGeorge syndrome (22q11.2) Non-allelic homologous recombination (NAHR) These LCR mediated rearrangements could lead to: – – – – – – a change in copy number of dosage-sensitive genes, gene disruption, creation of fusion genes, position effects, unmasking of recessive traits / functional polymorphisms or interruption of transvection (communication between alleles). Recurrent genomic rearrangements (such as deletions, duplications, isodicentric chromosomes and inversions) are usually caused by NAHR between LCRs. Can occur during meiosis or mitosis. Non-allelic homologous recombination (NAHR) At the molecular level, two mechanisms of NAHR have been proposed: Unequal crossing-over and BIR (Break-induced replication). – Unequal crossing-over is a recombination-based mechanism, – BIR is a replication-based mechanism. BIR occurs when a replication fork collapses or breaks and the broken molecule uses ectopic homology to restart the replication fork High copy repeats HCR such as Alu or satellite DNA sequences – 32 cases of single gene disorders and 16 cases of cancer have been attributed to Alu-recombination events – Interchromosomal non-allelic recombination events mediated by HCR satellite DNA sequences and/or other adjacent repetitive sequences located within the short arms of the acrocentric chromosomes, are hypothesised to be responsible for the formation of Robertsonian translocations DNA hotspots DNA hot spots for chromosome rearrangements has been supported by studies of recurring t(11;22) Breakpoints involved in this translocation are not associated with regions of homology, but with AT-rich palindromic sequences that are predicted to form hairpin-shaped secondary structures. These hairpin structures are thought to be susceptible to nucleases that produce double stranded breaks that serve substrates for recombination and formation of the resulting translocation – This mechanism has only been implemented in one other translocation t(17;22) Non-recurrent structural variants Characteristic features: – Scattered breakpoint locations – Unique to the carrying individual – Breakpoint junctions are often simple blunt ends Non-homologous end joining (NHEJ) Break induced replication (BIR) Microhomology-mediated break induced replication (MMBIR) Serial replication slippage (SRS) Fork-stalling and template switching (FoSTes) Balanced vs. unbalanced Balanced – No net loss or gain of genetic information (copy number neutral) – Individuals who carry them are generally phenotypically normal Unbalanced – Additional/absent genetic material (copy number gains or losses) – Some deviation from the normal phenotype Limits of conventional cytogenetics – Maximum level of resolution with G-banding is 2-5Mb – Cryptic abnormalities – Submicroscopic Associated risks Depend upon – Type of specimen it was found in – Clinical presentation e.g. Cancer or fertility studies Prenatal/children – Parental karyotypes should be obtained to assess whether it is de novo or inherited If de novo then the family would have a low risk of recurrence (gonadal mosaic) If a parent is a carrier then recurrence may be as high as 50% Reciprocal Translocations Most common structural rearrangement 1/1000 to 1/673 Carriers are phenotypically normal but have an increased risk of having children with unbalanced karyotypes due to malsegregation of the translocation Risk of abnormal phenotype in a de novo apparently balanced translocation is higher than if it is familial Possibility of gene disruption at the breakpoint(s) May represent an acquired change in certain cases Reciprocal Translocations t(11;22) t(11;22)(q23.3;q11.2) First recurring constitutional reciprocal translocation >100 apparently unrelated families have been reported with this abnormality Due to multiple independent translocation events between 2 susceptible regions of AT rich palindromic sequences (hot spots) Balanced carriers are phenotypically normal Phenotypically abnormal child as a result of 3:1 segregation error 47,N,+der(22)t(11;22)(q23;q11.2) ⇨supernumerary der(22) Emanuel syndrome (OMIM#609029, Gene Reviews PMID: 20301440)  Partial trisomy for the distal arm of chromosome 11 and proximal long arm of 22 MR, CHD, malformed ears, cleft palate, renal aplasia, genital abnormalities in males t(4;8)(p16;p23) has also been reported in unrelated families in the literature as the second recurring constitutional reciprocal translocation t(11;22)(q23;q11.2) 3:1 meiosis I malsegregation in the balanced translocation carrier. t(11;22)(q23;q11.2) 46,XY,t(11;22)(q23;q11.2) Robertsonian translocations Form when 2 long arms of any acrocentric chromosomes join to produce a single sub/metacentric chromosome Balanced carriers therefore have 45 chromosomes First described in 1916, by WRB Robertson Most common balanced structural rearrangements in the human population Frequency of approx. 1:1000 95% are nonhomologous – rob(13;14) is most common – rob(14;21) Reproductive risk – Increased risk of M/C and offspring with mental retardation and birth defects associated with aneuploidy and rarely UPD – Those with translocations involving 21 or 13 are associated with risk of a liveborn trisomic child, trisomy 22 is a rare possibility – der(15;21) carriers may have a predisposition to developing leukaemia (ALL) particularly in paediatric cases Robertsonian Translocation 1 4 13 Robertsonian translocation (Jorde et al, 2006) 45,XY,der(13;14)(q10;q10) Robertsonian Translocation Robertsonian - mechanism of formation 3 possible mechanism 1. Fusion at the centromere (centric fusion) 2. Union following breakage in one short arm and one long arm 3. Union following breakage in both short arms The common rob(13;14) and rob(14;21) translocations are practically always dicentric Inversions Two breaks within a single chromosome with the middle segment rotated 180° resulting in the reverse orientation of that segment. Terminology Pericentric Breakpoints lie on either side of the centromere Often changes the arm ratio (centromere position) Changes the banding pattern of the chromosome Paracentric Have both breakpoints on the same side of the centromere Centromere position does not change Often harder to detect Inversions inv(12)(q13.1q21.1) paracentric inv(5)(q22q33) paracentric Duplications Two breaks within one chromosome with the middle segment being doubled resulting in a net gain of genetic material. Most intrachromosomal duplications are presumed to arise de novo Recurrence risk is about 1% (except gonadal mosaics) Types – Direct (same orientation as its original position) – Inverted (reverse orientation from its original position) Compared with other rearrangements, a possibly higher frequency of mosaicism in the direct dup suggesting that post zygotic mechanism Duplications dup(1)(p21p22.1) dup(7) invdup(5) Duplication syndromes Syndrome region Duplication 3q 3q26.3 Beckwith-Weidemann 11p15.5 pat Pallister-Killian Mosaic tetrasomy 12p Dup 15q 15q11.2 mat Psuedodicentric 15 Tetrasomy 15pter-15q13 Dup 17p 17p11.2 Dup 22q 22q11.2 Cat eye Tetrasomy 22q11.2 Deletions Not all cause phenotypic abnormalities Loss p arms of acrocentrics Size of deletion DOESN'T CORRELATE WITH SEVERITY OF PHENOTYPE del 4p,5p seen in live births, del 19p fatal Terminology Interstitial: two breaks within one chromosome with the loss of the middle segment Terminal: single break within one chromosome with the loss of the distal/telomeric segment All stable chromosomes with apparent terminal deletions are assumed to have acquired new telomeres Deletion 5p – Cri Du Chat syndrome Deletions Deletion 4p – Wolf-Hirshhorn syndrome Interstitial deletion on chromosome 2p Deletions LCR Flanking LCR sequences have been found at the breaks of segmental aneuploidy syndromes. These sequences appear to provide recombination sites for unequal meiotic and mitotic exchange events. Lee et al. Neuron. 2006. PMID: 17015230 Segmental Aneuploidy Syndromes associated with flanking LCR Deletion syndrome Deleted region Monosomy 1p36 1p36 Wolf-hirschhorn 4p Cri du chat 5p Potocki- Shaffer 7q11.23 Jacobson 11p11.2 Langer-Giedion 8q24.1-8qter Angelman 15q11-13 mat Pradar-willi 15q11-13 pat Rubinstein-Taybi 16p13.3 Miller-Dieker 17p13.3 Smith-Magenis 17p11.2 Alagille 20p12 DiGeorge 22q11.2 Monosomy 22q13.3 22q13.3 Kallman Xp22.3 Ichthyosis Xp22.3 Ring chromosomes Autosomal rings are rare and usually arise de novo Frequency rates about 1 in 27000 to 6000 Rings have been reported for all chromosome pairs Those involving chromosome 13 and 18 are most common Rings can result in a partial monosomy for both long and short arm material If present as a supernumerary chromosome (ESAC), partial trisomy results Seen frequently in haemoncology investigations Ring chromosomes Formation Traditionally thought to form as a result of breakage in both arms of a chromosome with subsequent fusion of the ends and loss of the distal segments Recent molecular studies have suggested additional mechanisms Transverse misdivision of the centromere combined with a U-type exchange of one of the chromosome arms Telomere fusion: with no loss of genetic material Composed of discontinuous sequences Characteristics Instability Result from sister chromatid exchanges that occur within the ring chromosome before division Ring Formation Solid Stain Unbalanced r(2) Isochromosomes Is a mirror image chromosome, with 2 identical arms and 1 centromere Mode of formation Classical Misdivision at the centromere (centric fission) U type exchange Chromatid of one arm of a chromosome “looping around” to join with its fellow Isochromosome Formation Isochromosomes Dicentric Chromosomes Chromosome with 2 centromeres Most common type Robertsonian Other mechanism of formation Recombination within a paracentric inversion loop 2 active centromeres Potential for instability during division Solid Stain C band image idic(15)(q13) Recombinant Chromosomes These are generally the unbalanced result from unequal crossing over during meiosis Inverted chromosomes need to form a loop in order to pair correctly. Unequal cross overs in this loop formation result in imbalance. More common in pericentric inversions where the inverted segment is large. – Most often results in a “del/dup” scenario with a net loss and gain of genetics material. Recombinant Chromosome (paracentric inversion) Recombinant Chromosome (pericentric inversion) Large pericentric inversion in chromosome 2: inv(2)(p21q31)mat Unequal cross over in inversion loop formation Result in 2 different del/dup recombinants: rec(2)dup(2p)inv(2)(p21q31) rec(2)dup(2q)inv(2)(p21q31) Recombinant Chromosome (pericentric inversion) Unequal cross over in inversion loop inverted segment OR 2 inv(2) rec(2)dup(2p)inv(2)(p21q31) rec(2)dup(2q)inv(2)(p21q31) Insertions Are complex 3-break rearrangements that involve the excision of a portion of a chromosome from one site (2 breaks) and it’s insertion into another site (1 break) The orientation of the inserted segment can remain the same in relation to the centromere (direct) or be reversed (inverted) When the segment is inserted into a different chromosome is Interchromosomal Inserted into the same chromosome Intrachromosomal 3 break rearrangements are rare 1/5000 live births High risk of abnormal reproductive outcome Insertions Interchromosomal direct insertion Insertions: ins(2;10)(p25.1;q21.2q22.1) 10 2 “Jumping” translocations Dynamic or changing translocations that are rarely seen in constitutional karyotypes These can be seen as 2 types Mosaic state with different cell lines Different translocation between parent and child but with one common chromosomal breakpoint Breakpoints in jumping translocations frequently involve regions known to contain repetitive DNA sequences Telomeres, centromeres, nucleolar organisers Also thought to be a type of telomere healing by telomere capture Chromosomes require telomeres to be stable Case study 4 cell lines were identified in products of conception. Appears that chromosome 18 is involved in a jumping translocation at region p11.1 35% of cells contained a derivative chromosome 18 possibly formed by a translocation with chromosome 1 at region q41. 25% of cells contained an isodicentric chromosome 18 20% of cells had a chromosome 18 deleted at band p11.1. 20% of cells had a derivative chromosome 18 possibly formed by a translocation with chromosome 2 at region q32 46,XX,der(18)t(?1;18)(q41;p11.2) 1 2 3 6 7 8 13 14 15 19 20 9 21 4 5 10 11 12 16 17 18 22 X Y 46,XX,idic(18)(p11.1) 1 2 3 6 7 8 13 14 15 19 20 9 21 4 5 10 11 12 16 17 18 22 X Y 46,XX,del(18)(p11.1) 1 2 3 6 7 8 13 14 15 19 20 9 21 4 5 10 11 12 16 17 18 22 X Y 46,XX,der(18)t(?2;18)(q32;p11.1) 1 2 3 6 7 8 13 14 15 19 20 9 21 4 5 10 11 12 16 17 18 22 X Y Complex translocations Definition – A rearrangement involving 2 or more chromosomes and at least 3 breakpoints Rarely seen as constitutional, and those identified are are generally de novo in origin Complex translocations: 3 way translocation 10 15 1 46,XY,(1;15;10)(p13.3;q11.2;q22.3) Additional material “add” Often in chromosomal rearrangements there is additional material of unknown origin. – Segments where the banding pattern can not identified as being from a specific chromosome. Requires further molecular testing such as FISH or microarray to determine the origin. Parental bloods can also help determine if it is a derivative chromosome that has originated from a balanced rearrangement in a parent Additional material on chromosome 6 Acquired structural abnormalities – Translocations t(9;22)(q34;q11.2) BCR::ABL fusion gene – Deletions del(5)(q32) Haploinsufficiency of multiple gene – Duplications Dup 11q KMT2A gene involvement – Inversions inv(16)(p13q22) CBFB::MYH11 fusion gene Acquired structural abnormalities: example dup(1) add(2) del(11) t(8;14) 46,XY,dup(1)(p34p33),add(2)(p21),t(8;14)(q22;q32),del(11)(q21) ISCN Abbreviations Common nomenclature abbreviations used in cytogenetic written karyotypes chr t del add dup inv ins dic idic chromosome translocation deletion additional material duplication inversion insertion dicentric chromosome isodicentric chromosome i der rec rob isochromosome derivative chromosome recombinant chromosome Robertsonian translocation* *can also use der mar marker chromosome mat maternal pat paternal