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Results for “Chromosomes, Human, Pair 22”

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PubMed2003

Reevaluating human gene annotation: a second-generation analysis of chromosome 22.

We report a second-generation gene annotation of human chromosome 22. Using expressed sequence databases, comparative sequence analysis, and experimental verification, we have extended genes, fused previously fragmented structures, and identified new genes. The total length in exons of annotation was increased by 74% over our previously published annotation and includes 546 protein-coding genes and 234 pseudogenes. Thirty-two potential protein-coding annotations are partial copies of other genes, and may represent duplications on an evolutionary path to change or loss of function. We also identified 31 non-protein-coding transcripts, including 16 possible antisense RNAs. By extrapolation, we estimate the human genome contains 29,000-36,000 protein-coding genes, 21,300 pseudogenes, and 1500 antisense RNAs. We suggest that our revised annotation criteria provide a paradigm for future annotation of the human genome.

Animals↗

PubMed2019

The 22q11 low copy repeats are characterized by unprecedented size and structural variability.

Low copy repeats (LCRs) are recognized as a significant source of genomic instability, driving genome variability and evolution. The Chromosome 22 LCRs (LCR22s) mediate nonallelic homologous recombination (NAHR) leading to the 22q11 deletion syndrome (22q11DS). However, LCR22s are among the most complex regions in the genome, and their structure remains unresolved. The difficulty in generating accurate maps of LCR22s has also hindered localization of the deletion end points in 22q11DS patients. Using fiber FISH and Bionano optical mapping, we assembled LCR22 alleles in 187 cell lines. Our analysis uncovered an unprecedented level of variation in LCR22s, including LCR22A alleles ranging in size from 250 to 2000 kb. Further, the incidence of various LCR22 alleles varied within different populations. Additionally, the analysis of LCR22s in 22q11DS patients and their parents enabled further refinement of the rearrangement site within LCR22A and -D, which flank the 22q11 deletion. The NAHR site was localized to a 160-kb paralog shared between the LCR22A and -D in seven 22q11DS patients. Thus, we present the most comprehensive map of LCR22 variation to date. This will greatly facilitate the investigation of the role of LCR variation as a driver of 22q11 rearrangements and the phenotypic variability among 22q11DS patients.

22q11 Deletion Syndrome↗

PubMed2025

Optical mapping in Black genomes: Distinct LCR22 structures and 22q11.2 deletion syndrome mechanisms.

PURPOSE: The genomic architecture of 22q11.2 deletion syndrome (22q11.2DS) has primarily been studied in White populations, despite evidence suggesting a lower prevalence in Black individuals. This study aims to improve our understanding of the population-specific organization of 22q11.2 genomic structures. METHODS: Optical mapping data from 106 genomes, representing various Black and White individuals, were analyzed to assess the structure and variation of the 22q11.2 low copy repeats (LCR22s). RESULTS: Extensive variability in copy-number and orientation of LCR22 elements was observed between Black and White genomes. Several novel copy-number variants and haplotype configurations were identified, some being private or more prevalent within specific groups. Notably, copy-number variants diversity was particularly striking among Black genomes. Comparisons of Black and White families with de novo 22q11.2DS probands revealed unique nonallelic homologous recombination scenarios, with Black families exhibiting recombination patterns that are not previously observed. CONCLUSION: Perhaps the unique and highly variable LCR22 haplotype configurations in Black individuals contribute to the lower observed prevalence of 22q11.2DS by inhibiting the likelihood of nonallelic homologous recombination, the mechanism that leads to the syndrome.

Humans↗

PubMed1976

Detection of nucleolus organizer regions in chromosomes of human, chimpanzee, gorilla, orangutan and gibbon.

Nucleolus organizer regions were detected by the Ag-AS silver method in fixed metaphase chromosomes from human and primates. In the human, silver was deposited in the secondary constriction of a maximum of five pairs of acrocentric chromosomes: 13, 14, 15, 21 and 22. The chimpanzee also had five pairs of acrocentric chromosomes stained, corresponding to human numbers 13, 14, 18, 21 and 22. A gibbon had a single pair of chromosomes with a secondary constriction, which corresponded to the nucleolus organizer region. In each case the Ag-AS method detected the sites which have been shown by in situ hybridization to contain the ribosomal RNA genes. An orangutan had eight pairs of acrocentric chromosomes stained with Ag-AS, probably corresponding to human numbers 13, 14, 15, 18, 21 and 22, plus two others. Two gorillas had silver stain over two pairs of small acrocentric chromosomes and at the telomere of one chromosome 1. The larger gorilla acrocentric chromosomes had no silver stain although they all had secondary constrictions and entered into satellite associations.

Animals↗

PubMed1979

A case of trisomy 22 in Pongo pygmaeus.

A behaviorally and clinically abnormal female orangutan was analyzed cytologically using general banding techniques and by an alkaline silver method for staining nucleolus organizer regions. The karyotype had 49 chromosomes, including an extra chromosome 22 (49,XX + 22). No variant chromosome types or heterozygous structural rearrangements were found. Nine of the 14 large acrocentric chromosomes, Nos. 11--17, and three of the five presumptive human G-group equivalents, i.e., two of three chromosomes 22, and one chromosome from pair 23, exhibited positive silver staining of the nucleolus organizer region (NOR).

Animals↗

PubMedDate not supplied

[Intraspecies variability of the normal human karyotype].

On the basis of data from literature the number of different normal structural variants of each human chromosome is calculated. Assuming independent combination of chromosome variants, the number of possible combinations of variants of all 22 pairs of autosomes and the probability of an individual to be hormozygous for the most frequent variants of all the autosome pairs simultaneously are estimated. The results obtained show that nearly each individual possesses a unique karyotype--a unique set of properties of chromosome heterochromatic regions.

Chromosomes, Human↗

PubMed1977

The nucleolar cycle in man.

Tissue cultures of human embryonal kidney and ovary were examined. In the nuclei of both tissues, one to ten nucleoli have been found. The maximum number of nucleoli is connected with the gene expression of rDNA of the 10 nucleolus organizers of chromosome pairs Nos. 13, 14, 15, 21 and 22, which have secondary constrictions and are the satellite chromosomes in man. The small percentage of cells with 10, 9 and 8 nucleoli is attributed to the rapid association of 3 of the homologous acrocentrics (perhaps of group D). Two of the satellite (SAT) pairs probably associate later after mitosis. The process of fusion is dynamic, resulting in one interphase nucleous--a manifestation of the association of all SAT chromosomes. Dissociation of the nucleolus occurs upon entering prophase, due to the condensation of the chromosomes and retreat of rDNA to the respective secondary constrictions. As a result, the nucleolar number increases again. The pattern of the nucleolar kinetics within the course of one mitotic division is described.

Cell Nucleolus↗

PubMed1976

[Sequential staining for G- and C-banding of chromosomes in the analysis of the morphology of the short arms of human acrocentric chromosomes].

Sequential staining for G- and C-banding of acrocentric chromosomes of 8 persons showed that the large heterochromatin region occurred more frequently in chromosome 15 than in chromosomes 13 and 14, and in chromosome 22 more frequently than in chromosome 21. There proved to be no correlation between the size of the heterochromatic region and the short arm of the acrocentric chromosomes. The frequency of occurrence of the satellites in the 8 persons was approximately the same for all the acricentric pairs. The C-banded satellite region of the homologous chromosomes is often heteromorphic.

Chromosome Aberrations↗

PubMed1979

Application of a recombination model in calculating the variance of sib pair genetic identity.

Using a previously described model of crossing over (Risch & Lange, 1979), we have calculated analytically the variance in the proportion of genes identical by descent shared by two sibs. The prior distributions for numbers of chiasmata reported in Suarez et al. (1979) were used to calculate a standard deviation of 0.040 for the 22 human autosomes. It is also shown that any two identity by descent values within a sibship are uncorrelated.

Animals↗

PubMed2025

Molecular features influencing clinical outcome of advanced HER2-positive gastric cancer receiving trastuzumab plus chemotherapy.

BACKGROUND: Less than half of the human epidermal growth factor receptor 2 (HER2)-positive gastric cancer (GC) patients respond to trastuzumab plus chemotherapy, and the outcomes are unsatisfactory. Understanding the underlying mechanisms remains crucial for identifying patients who are more likely to benefit from treatment. PATIENTS AND METHODS: We performed targeted DNA sequencing on paired pre-treatment and progressive tumour tissues from 22 HER2-positive advanced GC patients undergoing first-line treatment with trastuzumab and chemotherapy. Clinicopathological and genomic characteristics were assessed for the correlation with clinical outcomes. RESULTS: A performance status (PS) of 0-1 was associated with improved progression-free survival (PFS) and overall survival (OS) than a PS of 2. Poorly differentiated tumours exhibited shorter PFS than moderate or moderate-poor ones. Pre-treatment amplification of MYC or TOP2A gene was association with increased PFS, and suggested a potential benefit for OS. Patients with higher tumour mutation burden (TMB) experienced significantly worse PFS, while higher chromosome instability (CIN) appeared to be correlated with longer PFS. Compared to non-responders, responders had a higher CIN but similar TMB and intratumoural heterogeneity (ITH). PS and MYC amplification emerged as independent factors related to PFS according to multivariate survival analysis. Additionally, after treatment, TMB significantly increased in non-responders, while CIN significantly decreased in responders. CONCLUSIONS: Pre-treatment MYC amplification and PS were independently associated with clinical outcomes in HER2-positive advanced GC patients treated with first-line trastuzumab plus chemotherapy. Dynamic post-treatment changes in TMB and CIS provide valuable insights into the relationship between therapeutic response and distinct evolutionary trajectories.

Humans↗

PubMed1977

Frequency of Ag-stained nucleolus organizer regions in the acrocentric chromosomes of man.

The Ag-stainability of the nucleolus organizer region (NOR) was studied in the acrocentric chromosomes identified by Q-banding of cultured lymphocytes in 51 karyotypically normal persons (31 males and 20 females). A consistent pattern of Ag-positive NORs was found in each individual. Ninety percent of individuals have a model number of 8--10 Ag-positive NORs per cell. The frequency of Ag-positive NORs is similar in all five acrocentrics. A statistically nonsignificant lower frequency is found in chromosome 22. Ag-negative NORs on both homologues were found in four cases. The observed frequency distribution of individuals with homozygous NOR-positive, heterozygous, and homozygous negative acrocentric chromosomes was in accordance with the Hardy-Weinberg law in all five pairs of the acrocentric chromosomes as well as in total. No sex difference was observed on our material.

Cell Nucleolus↗

PubMed1977

Cytogenetic investigation in twins with manic-depressive disorders (22 monozygotic and 27 dizygotic twin pairs).

Chromosome examination was made in 22 monozygotic and 27 dizygotic twin pairs of whom one or both of each pair suffered or had suffered from manic-depressive disorder. We found a significantly higher frequency of chromosome variations among dizygotic twin pairs than was expected from population studies, but not in monozygotic pairs. There was no association between the chromosome variations and manic-depressive disorders. We found no greater intra-pair correlation in monozygotic twins compared with dizygotic twins as regards hypodiploidy, hyperdiploidy and unstable chromosome aberrations, which indicates that the aetiology of such aberrations is mainly of exogenic nature.

Bipolar Disorder↗

PubMed1979

A mutation which alters initiation of transcription by RNA polymerase III on the Ad5 chromosome.

Mutant dl 309 is a viable Ad5 deletion mutant. Whereas wild-type Ad5-infected HeLa cells contain two VAI RNA species [VAI(A) and VAI(G)] which differ by three nucleotides at their 5' ends, dl 309-infected HeLa cells contain VAI(G) but no VAI(A) RNA. Nucleotide sequence analysis indicates that dl 309 lacks two base pairs which precede the 5' end of VAI(A) by 22 nucleotides. Since the 5' ends of VAI RNAs are not processed, the 309 deletion serves to identify a portion of the sequence required for RNA polymerase III initiation. Since dl 309 grows as well as wild-type Ad5 in HeLa cells, the VAI(A) species is not essential for viral growth in these cells.

Adenoviruses, Human↗