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PubMed2026

Adaptive deletion of functional duplicate genes in Drosophila.

Gene deletion is traditionally viewed as a nonadaptive mechanism that eliminates functional redundancy, yet emerging evidence indicates that it disproportionately affects tissue-specific duplicates with unique functions. Here, we test whether gene deletion preferentially removes weakly constrained, degenerating duplicates or instead eliminates functionally active duplicates through an adaptive process. To identify the evolutionary and functional factors that determine which duplicates are lost, we systematically analyzed 100 gene deletion events in Drosophila by integrating sequence, expression, interaction, and structural data. We uncovered a strong bias toward the loss of younger child copies among functionally unique duplicates, whereas no such bias was observed for redundant duplicates. Contrary to expectations under relaxed constraint, deleted functionally unique genes evolve more slowly, show higher expression, engage in more protein-protein interactions, and do not exhibit elevated structural divergence or intrinsic disorder relative to redundant duplicates. When compared with single-copy genes, deleted functionally unique genes display similar evolutionary rates, slightly lower expression, greater network connectivity, comparable structural divergence, and lower intrinsic disorder. These patterns suggest that deletion frequently affects functionally active rather than degenerate genes. Collectively, our results support the hypothesis that gene deletion in Drosophila can represent an adaptive process acting on transiently functional duplicates, potentially driven by either genome streamlining or context-dependent deleterious effects.

evolution↗

PubMed1979

Partial monosomy 7 with interstitial deletions in two infants with differing congenital abnormalities.

Two cases of interstitial deletion of chromosome 7 are presented, one involving the short arm and the other the long arm. The cytogenetic, dermatoglyphic, and clinical findings are compared with previously reported cases of chromosome 7 deletion. The patient with a short arm deletion differs clinically from the previously reported cases but, in common with a least one previous case, has a low total finger ridge count. His interstitial deletion involving the 7p13 leads to 7p21 region also differs from 7p deletions reported in earlier cases. The patient with a long arm deletion has an interstitial loss of the region between 7q11 and 7q21, corresponding to one of three groups of 7q deletion that have been recognised. The phenotypic changes in this group are less well defined than in the other two and the patient presented here differs clinically from the previously reported cases, apart from one phenotypically normal mosaic case, in lacking morphological abnormalities. He shares with one previous case both epilepsy and a high intensity of dermal ridge patterns.

Abnormalities, Multiple↗

PubMed1979

Deletions, rearrangements and tandem duplications of recombinant plasmids containing yeast ribosomal DNA.

Recombinant DNA plasmids, formed by the insertion of yeast ribosomal DNA into Escherichia coli plasmids pSC101 or pMB9, underwent deletions, rearrangements and tandem duplications. Independently derived deletion products of plasmids, constructed using pMB9 as a vector, are indistinguishable from each other. These deletion products from multimers composed of tandem repeats. In at least one case a plasmid, constructed by inserting an SmaI fragment of yeast ribosomal DNA into pSC101, underwent deletion and rearrangement to form a product in which a segment, consisting of part of the pSC101 sequence and part of the yeast ribosomal DNA sequence, was duplicated to form a tandem repeat. Deletion and rearrangement take place in Rec+, recA- and recB- recC- cells. The rate of deletion in Rec+ cells is higher than in recA- cells. The rate of deletion in minicell-producing, X-ray resistant strains is much higher than in other Rec+ strains.

Chromosome Deletion↗

PubMed1977

Deletions of two heat-activated loci in Drosophila melanogaster and their effects on heat-induced protein synthesis.

Deficiencies that delete two heat-induced puffs in Drosophila melanogaster have been isolated. Two deficiencies delete the puff arising from 87C1, and one deletes the two puffs at 87A and 87C1. Homozygotes for these deletions can be recognized by their abnormal, transparent malpighian tubules. The influence on heat-induced protein synthesis of deleting one or both of these puffs has been examined. Unexpectedly, deleting only the 87C1 puff has no apparent effect. Deleting both the 87A and 87C1 puffs eliminates synthesis of a 71,000 dalton protein. We map a coding locus for the 71,000 dalton heat-induced protein to 87A7-B3, a seven band region which also contains a heat-induced puff. The roles of the 87A and 87C1 puffs in coding for heat-induced proteins are discussed in the light of these results.

Animals↗

PubMed1979

Deletion mutant of the Bratislava-77 strain of Rous sarcoma virus containing a fusion of the group-specific antigen and envelope genes.

The genetic compositions of two independently derived preparations of the Bratislava-77 strain (B77) of Rous sarcoma virus were analyzed after each was passaged seven or more times in duck embryo fibroblasts. RNase, T1-resistant oligonucleotide fingerprint analysis of virion RNA from both preparations of duck-passaged B77 revealed the presence of two large noncontiguous deletions. Approximately 75% of the RNAs contained a deletion which spans oligonucleotides 304 to 4 on the viral genome (about 3,500 nucleotides) and encompasses all of the B77 polymerase gene. More than 90% of the RNAs also contained a deletion which spans src-specific oligonucleotides 6 and 5(about 2,200 nucleotides) and is identical to the deletion observed in transformation-defective B77. Virion RNA from duck-passaged B77 also contained two oligonucleotides (D1 and D2) not observed in the RNA of B77 virus grown on chicken embryo fibroblasts. Analysis of the virion RNA of duck-passaged B77 by denaturing agarose gel electrophoresis revealed four major subunits with molecular weights of 3.40 x 10(6), 2.65 x 10(6), 2.25 x 10(6), and 1.55 x 10(6). Whereas the 3.40- and 2.65-megadalton (Mdal) RNA species comigrated with the nondefective and transformation-defective RNAs of B77 propagated on chicken embryo fibroblasts, no counterparts to the 2.25- and 1.55-Mdal RNAs were observed in the RNA of B77 grown on chicken embryo fibroblasts. Oligonucleotide fingerprint analysis of these RNA species revealed that the 2.65-Mdal RNA contains the src-specific deletion and that 2.25-Mdal RNA contains the polymerase region deletion; both of these deletions were observed in the 1.55-Mdal RNA, which was the major RNA subunit species detected in duck-passaged B77. The new oligonucleotides (D1 and D2) observed in the duck-passaged virus were present in the 2.25- and 1.55-Mdal RNA species in vitro and in vivo and directs the synthesis of a 130,000-dalton protein (p130). p130 contains antigenic determinants specific for p27 (gag gene) and gp85 (env gene) but does not contain sequences which cross-react with antisera directed against the alpha beta form of RNA-dependent DNA polymerase (pol gene). This RNA, therefore, is generated by a fusion of the gag and env genes of Rous sarcoma virus B77.

Antigens, Viral↗

PubMed2025

A common DNA deletion altering the 3'UTR of mdr1 is associated with reduced mefloquine susceptibility in P. vivax parasites from Cambodian patients.

Artemisinin-combination therapies (ACTs) are now recommended for the treatment of uncomplicated malaria caused by Plasmodium vivax, the parasite responsible for the majority of malaria infections outside of Africa. We analyzed the genome sequences of 206 P. vivax parasites collected from Cambodian malaria patients and showed that more than 80% of them carried a DNA deletion located immediately downstream of the multidrug resistance 1 gene (mdr1). This 837 bp deletion overlapped with a different deletion present at low frequency in South American isolates, suggesting a functional role despite not altering the coding sequence of mdr1. Using RNA sequencing, we showed that these deletions altered the transcripts expressed from mdr1 and resulted in mRNAs with different 3' untranslated regions. In Cambodian isolates, the deletion was significantly associated with a higher expression of mdr1 and a lower ex vivo susceptibility to mefloquine. Finally, we genotyped 592 Cambodian isolates collected between 2014 and 2024 and showed that the mdr1 deletion increased in frequency in Cambodia since the introduction of mefloquine as ACT partner drug. Overall, these findings indicate that a common deletion of a non-coding sequence affects the transcription, stability, or translation of mdr1 in P. vivax parasites and could mediate reduced susceptibility to antimalarial drug(s) currently used for the treatment of uncomplicated vivax malaria.

Journal Article↗

PubMed2026

Clinical outcomes and genomic features of uncommon EGFR exon 19 deletion subtypes in osimertinib-treated non-small cell lung cancer.

BACKGROUND: Epidermal growth factor receptor (EGFR) exon 19 deletion subtypes may be associated with differential survival outcomes following EGFR-tyrosine kinase inhibitor treatment. However, evidence remains scarce, particularly regarding osimertinib, and the underlying biological mechanisms are poorly understood. We aimed to compare survival outcomes among EGFR exon 19 deletion subtypes in patients with non-small cell lung cancer (NSCLC) treated with osimertinib. METHODS: In this multicenter retrospective study, patients with NSCLC were stratified according to exon 19 deletion subtypes. Whole-exome sequencing data from the American Association for Cancer Research Genomics Evidence Neoplasia Information Exchange registry and Memorial Sloan Kettering Clinicogenomic Harmonized Oncologic Real-World Dataset were analyzed to investigate co-occurring genomic alterations. RESULTS: Overall, 111 patients with advanced EGFR exon 19 deletion-positive NSCLC were analyzed and 86.5% received osimertinib as first-line therapy. Patients with non-E746_A750del (n = 25) had shorter progression-free survival (PFS) than those with E746_A750del (n = 86) (median: 14.3 vs. 20.6 months; p < 0.05). Among non-E746_A750del subtypes, L747_A750delinsP (n = 4) had a particularly poor prognosis, with significantly worse survival than those with E746_A750del (median PFS: 3.5 vs. 20.6 months; p < 0.001, and median overall survival: 11.8 vs. 48.5 months; p < 0.001). In public database analyses, non-E746_A750del had a higher rate of RBM10 co-mutations, whereas L747_A750delinsP was characterized by frequent CDKN2A/B homozygous deletions and MYC amplifications. CONCLUSIONS: Non-E746_A750del was associated with poorer outcomes, with L747_A750delinsP potentially being a high-risk subtype. Differences in co-occurring genomic alterations may contribute to the prognostic heterogeneity among exon 19 deletion subtypes.

Humans↗

PubMed2026

Plasmodium falciparum Parasites With Histidine-Rich Protein 2 (pfhrp2) and pfhrp3 Gene Deletions in Frontier Endemic Regions of Brazilian Amazon.

Studies reporting deletions of the pfhrp2 and pfhrp3 genes in P. falciparum populations in various malaria-endemic countries, including countries bordering Brazil, are increasing. Individuals infected with P. falciparum carrying deletions of the pfhrp2/3 genes may yield false-negative results in Rapid Diagnostic Tests (RDTs) based on the detection of these antigens. A total of 342 samples from symptomatic individuals infected with P. falciparum, collected during epidemiological surveillance activities in the municipalities of the international frontier between Brazil and Peru and between Brazil and Venezuela were analysed. Of the 342 samples evaluated, 86 (25.2%) showed pfhrp2-deletion, 32 (9.4%) double deletions of the pfhrp2/3 genes, and 168 (49.1%) had a single deletion of the pfhrp3 gene. The frequency of parasites with pfhrp2/3 deletions highlights the importance of genomic surveillance in international border areas, alongside the evaluation of the effectiveness of RDTs used in the country.

pfhrp2↗

PubMed2026

Clinical and Genetic Spectrum of Large AIP Deletions.

Familial isolated pituitary adenoma (FIPA) accounts for approximately 2%-5% of all pituitary adenomas, with inactivating variants of the aryl hydrocarbon receptor-interacting protein (AIP) gene representing the most frequent known genetic cause. Clinically, patients with AIP variants often have young-onset macroadenomas with growth hormone hypersecretion, although disease severity and penetrance are variable. Most reported AIP variants are point mutations, whereas large deletions are rare and potentially underdiagnosed. Accurate detection of AIP copy-number variants requires methods such as multiplex ligation-dependent probe amplification or validated copy-number analysis of next-generation sequencing data, as Sanger sequencing alone may fail to identify these alterations. Due to the rarity of the disease, it is unknown whether large deletions in the ubiquitously expressed AIP gene are associated with potentially more severe phenotype. Available data suggest that large deletions may occur in 8%-10% of AIP mutation-positive pedigrees, highlighting the importance of incorporating copy-number variant detection into AIP testing workflows. We analysed data from all published patients with large AIP deletions (n = 25) and report here two novel large AIP deletions (Exons 3-4 and Exons 2-6 deletions) and three additional three families, including an Albanian kindred associated with metastatic Hürthle cell thyroid carcinoma. No major differences compared with other AIP variants were found in age at diagnosis, tumour size, hormonal profile, sex distribution or presence of other tumours. A role for AIP variants in thyroid carcinogenesis is unlikely.

Humans↗

PubMed2026

Distinct cerebellar and inner-ear phenotypes in Atoh1 promoter-proximal deletion mice.

OBJECTIVE: Atoh1 is essential for the development of the cerebellum and inner ear, but the in vivo role of its promoter-proximal region remains incompletely understood. We generated deletion lines targeting the Atoh1 promoter-proximal region containing C sites and examined their phenotypes in the cerebellum and inner ear. METHODS: Using the CRISPR-Cas9 genome editing method, mice with deletions in the Atoh1 promoter-proximal region containing C sites were generated, and four independent deletion lines were established. Gross morphology and histology of the cerebellum and inner ear were examined in 2-month-old mice. RESULTS: Four independent deletion alleles were obtained and designated line A to line D in ascending order of deletion size. In the cerebellum, gross examination and sagittal sections showed progressively more severe hypoplasia from line A to line D, accompanied by reduced foliation and disorganization of cortical architecture. The granule cell layer was progressively reduced, whereas Purkinje cells were relatively preserved. Behavioral abnormalities were detected only in the most severely affected line. In the inner ear, the maculae of the otolith organs were relatively preserved across all lines. The ampullary cristae were relatively preserved in lines A-C but showed hair-cell loss in line D. Cochlear phenotypes were more severe: line A retained relatively preserved inner hair cells with reduced outer hair cells, whereas lines B-D showed near-complete loss of hair cells and marked disruption of the organ of Corti in the analyzed regions. Descriptive quantitative analyses of available specimens supported progressive cerebellar hypoplasia, relative macular preservation, line D crista involvement, and severe cochlear hair-cell loss in lines B-D. CONCLUSION: Deletion of the Atoh1 promoter-proximal region produced distinct tissue-specific phenotypes in vivo. These findings suggest that the Atoh1 promoter-proximal region is differentially required in the cerebellum and inner ear and that its contribution varies among vestibular and cochlear sensory organs.

Atoh1↗

PubMed1977

Deletions affecting the transposition of an antibiotic resistance gene.

The structural gene for plasmid-mediated ampicillin resistance resides upon a 3.2 X 10(6) dalton transposable sequence (TnA) flanked by short inverted repeated sequences that accompany its insertion. TnA was transposed to pMB8, a 1.8 X 10(6) dalton derivative of the colicingenic plasmid ColE1. Random deletions were introduced in the resultant 5 X 10(6) dalton recombinant plasmid by a combination of nuclease treatments in vitro. From this set of deletions a subset was isolated that contained deletions affecting the transposition of TnA. The deletions were mapped by digestion with restriction nucleases and electron microscopic analysis of DNA hetero-duplexes and were found to include one of the inverted repeated sequences or lie in the central portion of TnA. Complementation experiments were attempted between these plasmids and another compatible plasmid carrying a deletion in TnA that abolished its ampicillin resistance. The results of the deletion data indicate that approximately 2 X 10(6) daltons of TnA is required for transposition; the complementation experiments suggest that the terminal inverted repetition and the central region of TnA play different essential roles in TnA transposition.

Crosses, Genetic↗

PubMed1977

Biochemical genetics of the alpha-keto acid dehydrogenase complexes of Escherichia coli K12: isolation and biochemical properties of deletion mutants.

Mutants of Escherichia coli K12 with deletions in the nadC-lpd region of the chromosome were obtained for use in studies on the expression of the ace (pyruvate dehydrogenase complex, specific components) and lpd (lipomide dehydrogenase) genes. These were isolated by selecting spontaneous aroP mutants (lacking the general aromatic amino-acid permease and thus resistant to inhibitory aromatic amino-acid analogues) and screening for auxotrophy due to deletions extending into neighbouring genes. From 2892 isolates tested, the AroP- phenotypes of 2322 were confirmed and, of these, 28 stable and independently-derived auxotrophos were designated as deletion mutants. Six nutritionally-distinct categories were recognized: Nad- (8 strains); Nad-Ace-(7): Nad-'Ace-' (3); Ace- (8); 'Ace-' (I); Lpd-(I). The Ace- phenotypes of four isolates designated 'Ace-' were leaky and enzymological studies confirmed that they had less than 7% of parental pyruvate dehydrogenase complex activity. Enzymological studies showed that the 15 Ace- or Nad-Ace- strains all lacked the pyruvate dehydrogenase complex and pyruvate dehydrogenase (EIp) activities and only three retained detectable dihydrolipoamide acetyltransferase (E2p). The one Lpd- strain lacked pyruvate dehydrogenase, dihydrolipoamide acetyltransferase and lipoamide dehydrogenase (E3) activities as well as the activities of the pyruvate and alpha-ketoglutarate dehydrogenase complexes. The results confirmed the gene order nadC-aroP-aceE-aceF-lpd and indicated that no other essential functions are determined by genes within the nadC-lpd region. Resistance to lactate during growth of pps mutants on acetate was directly related to the specific activity of the pyruvate dehydrogenase complex. None of the deletions promoted the high degree of resistance characteristically associated with constitutive expression of the dehydrogenase complex. Six pps mutants having Ace+ or 'Ace-' phenotypes were more sensitive than the parental strains and expression of their ace operons appeared to be affected; most sensitive were the Ace- strains which lacked pyruvate dehydrogenase complex and phosphoenolpyruvate synthetase activities. The lipoamide dehydrogenase activities of the deletion strains (Lpd+) ranged between 30% and 100% of parental levels indicating that expression of their ace operons appeared to be affected; most sensitive were the Ace- strains which lacked pyruvate dehydrogenase complex and phosphoenolpyruvate synthetase activities. The lipoamide dehydrogenase activities of the deletion strains (Lpd+) ranged between 30% and 100% of parental levels indicating that expression of the lpd gene may be affected by the ace operon but can be independent.

Dihydrolipoamide Dehydrogenase↗

PubMed1979

Nucleotide sequence analysis of two simian virus 40 mutants with deletions in the late region of the genome.

Two mutants of simian virus 40, dl-1261 and dl-1262, have deletions that map between coordinated 0.90 and 0.95 (Cole et al., J. Virol 24:277--294, 1977). Both affect the structure of the two minor proteins VP2 and VP3. The precise location and size of the deletions have now been determined by nucleotide sequence analysis. Mutant dl-1261 is deleted of 54 base pairs, is temperature sensitive for the protein defined by the D complementation group, and promotes the synthesis of shorter VP2 and VP3 polypeptides. Mutant dl-1262 is viable irrespective of temperature and has a deletion of 36 base pairs, 23 of which overlap the deletion in dl-1261. Since these mutants produce normal VP1, the deleted regions probably have no function in the splicing of precursor RNA to the VP1 mRNA.

Base Sequence↗

PubMed2026

Enhancing Hemoglobin Bart's hydrops fetalis syndrome prevention: a single-tube multiplex real-time PCR assay for the comprehensive detection of four significant α0-thalassemia deletions (--SEA, --THAI, --CR, and --SA) found in Thailand.

BACKGROUND: Hemoglobin (Hb) Bart's hydrops fetalis is a major public health concern in Southeast Asia, particularly in Thailand. Current screening strategies target the two most common α0 -thalassemia deletions (--SEA and --THAI). METHOD: In this study, we developed a single-tube multiplex real-time PCR assay for the simultaneous detection of four clinically relevant α0-thalassemia deletions (--SEA, --THAI, --CR, and --SA). The assay was validated using 538 clinical samples with diverse thalassemia genotypes and compared against conventional gap-PCR as the reference method. Analytical performance, including sensitivity, specificity, and limit of detection (LOD), was evaluated. In addition, clinical utility was assessed in 22 prenatal diagnosis cases at risk of Hb Bart's hydrops fetalis. RESULTS: The study cohort demonstrated substantial genetic heterogeneity, comprising 43 distinct genotypes. The developed assay achieved 100% sensitivity and specificity for all targeted deletions, with complete concordance with gap-PCR results. No cross-reactivity was observed with α+-thalassemia. The assay demonstrated a high analytical sensitivity with a LOD of 9.76 × 10-3 ng per reaction. Whereas in prenatal diagnosis, all 22 fetal genotypes were accurately identified, including five cases of homozygous --SEA and one rare compound heterozygous --SEA/--CR fetus. CONCLUSIONS: This study presents a rapid, accurate, and cost-effective multiplex real-time PCR assay capable of detecting both common and rare α0-thalassemia deletions in a single reaction. The assay demonstrates strong potential for implementation in routine clinical laboratories and large-scale population screening, contributing to improved prevention and control of severe thalassemia syndromes in high-prevalence regions.

Humans↗

PubMed1979

Syndromes associated with deletion of the long arm of chromosome 18[del(18q)].

We studied eight persons whose karyotypes demonstrated deletion of a portion of the long arm of chromosome 18. Seven of these persons who showed the typical del(18q) syndrome had a common deletion in band 18q21, most likely band q21.3, and in at least two persons the deletion was interstitial. Another mentally retarded child, dissimilar in appearance, had a more proximal deletion within band 18q12. Two different clinical syndromes resulted from deletions of these different segments of the long arm of chromosome 18.

Abnormalities, Multiple↗

PubMed1979

DNA sequence alterations in Hr-t deletion mutants of polyoma virus.

We have investigated the DNA sequence alterations in several hr-t mutants of polyoma virus. These mutants are defective in one of the two known viral functions essential for transformation and are altered with respect to several minor T antigen species. The lesions in some of these mutants have been mapped previously by marker rescue experiments to Hpa II fragment 4 (Hpa II-4, 78.4--91.7 map units) in the proximal part of the early region of the viral DNA. Thirteen of sixteen hr-t mutants examined carry deletions 2 to 5 map units (100--250 bp) long in Hpa 11-4. Three mutants carry either point mutations or very small deletions/insertions. Eight of the deletion mutants were mapped closely with restriction enzymes. Seven of them have deletions located entirely within the Hae III subfragment A of Hpa II-4 (the Hae A subfragment, 78.4--85.2 map units), and one extends just beyond this subfragment, ending at 85.5 map units. The complete sequence of the wild-type Hae A subfragment was determined and compared with those of four deletion mutants, NG-18, A-8, 6B5 and B-2. The deletion in each of these mutants is out-of-phase: NG-18, 187 bp; A-8, 127 bp; 6B-5, 179 bp; B-2, 241 bp. All are expected to remove protein sequences in the C terminal part of the small t antigen.

Amino Acid Sequence↗

PubMed1979

Biogenesis of poxviruses: mirror-image deletions in vaccinia virus DNA.

Restriction endonuclease analysis of viral DNA extracted from wild-type and temperature-sensitive mutants of vaccinia IHD-W (Dales et al., 1978) revealed sequence alterations in approximately 20% of all ts clones examined. The rearrangements were due to deletions up to 250 nucleotide pairs long. Using Eco RI, Sal I, Bam I, Hpa I and Ava I, the deletions were always observed in the same fragments, while analysis with Hind III demonstrated deletions of identical size in the two terminal fragments. Since vaccinia virus contains inverted terminal repeats of more than 10 kb, these clones possess identical deletions of opposite orientation at both ends of the genome. Analysis of several revertants of the ts mutants demonstrated that the deletions probably arise as events independent from those producing ts lesions and are generated spontaneously at high frequency. This implies that a single event during replication caused the elimination of nonessential information, and suggests that circular intermediates must exist transiently during viral replication.

Base Sequence↗

PubMed1979

Characterisation of deletions which affect the expression of fetal globin genes in man.

Deletions in the DNA of individuals with hereditary persistence of fetal haemoglobin (HPFH) and 8 beta-thalassaemia have been mapped as a means of identifying regulatory sequences involved in the switch from fetal to adult globin gene expression. The end points of these deletions have been precisely located with respect to restriction endonuclease cleavage sites within and surrounding the gamma-, delta- and beta-globin genes in normal human DNA and the deletion maps were used to obtain definitive evidence for the physical linkage of the fetal and adult beta-like globin genes in the order 5'Ggamma-Agamma-delta-beta 3'. Correlation of haematological data and the location of deletions in two cases of HPFH and one case of deltabeta-thalassaemia suggest that a region of DNA located near the 5'-end of the delta-globin gene may be involved in the suppression in cis of gamma-globin gene expression in adults. The interpretation of a second case of deltabeta-thalassaemia is complicated by the fact that the deletion removes the Agamma-gene in addition to the region near the 5'-end of the delta-globin gene.

Chromosome Deletion↗