Search PubMed⌕ Search

SEARCH · Search PubMed

Results for “genomic evaluation”

Search indexed PubMed citations on genomics, clinical trials, systematic reviews and public health. Explore titles, authors and supplied subject terms, then open the PubMed record.

Quote a phrase for an exact phrase match. Source license links do not imply unrestricted reuse.

At least 55 records · Page 3Linked to original sources
PubMed2003

Genome size variations in diploid African Coffea species.

Flow cytometry was conducted to evaluate genome size diversity among African diploid species of the Coffea genus. The study included 15 species and six new taxa from Congolese and Cameroonian forest regions which have yet to be botanically characterized. Between-population differences were also recorded in some cases. These evaluations using an internal standard were highly correlated with previous results obtained with an external standard, but differences of up to 18 % existed for some species, involving stoichiometric errors. Consequently, genome size variation between species and within species are discussed as true genome size differences or stoichiometric errors. Environmental and phenotypic correlations with genome size are also discussed.

Africa, Central↗
PubMed2000

Complex germline rearrangement of BRCA1 associated with breast and ovarian cancer.

Germline mutations in BRCA1 predispose to breast and ovarian cancer. Most germline BRCA1 mutations are small insertions, deletions, or single base pair (bp) substitutions. These mutation classes are rarely found as somatic mutations in BRCA1. On the other hand, somatic deletions of multiple mega-base pairs (Mb) including BRCA1, as reflected by loss of heterozygosity, occur frequently in both inherited and sporadic breast and ovarian cancers. To determine whether deletions or rearrangements of hundreds to thousands of bps might contribute to inherited mutation in BRCA1, we developed a Long PCR strategy for screening the entire genomic BRCA1 locus in high-risk families. We evaluated genomic DNA from one high-risk family of European ancestry with BRCA1-linked cancer in which no genomic mutations had been detected using conventional methods. Long PCR revealed a complex mutation, g.12977 ins10 del1039 (based on GenBank L78833), comprising an inverted duplication and deletion in BRCA1 that removes portions of exon 3 and intron 3, including the 5' splice site for intron 3. As a result of the deletion, exon 3 is skipped, leading to a truncated protein and disease predisposition. Unlike previously reported large germline deletions in BRCA1, neither breakpoint resides within an Alu element. The g.12977 ins10 del1039 mutation was not detected among 11 other breast cancer families, nor among 406 breast cancer patients unselected for family history.

Alu Elements↗
PubMed2026

LAMBDA: a prophage detection benchmark for genomic language models.

Transformer-based genomic sequence models represent an emerging frontier in computational biology. Yet, their embeddings have not yet shown the same level of predictive power as natural and protein language models, highlighting a gap between current implementations and theoretical promise. Existing benchmarks for DNA language models primarily focus on classifying regulatory elements in eukaryotic genomes, leaving open the fundamental question of whether these models learn sequence-level features across whole genomes. We introduce LAMBDA, a benchmark designed to rigorously evaluate genome language model embeddings through phage-bacteria sequence discrimination across four categories of increasing complexity: probing tasks, fine-tuning assessments, diagnostic tests, and genome-wide prophage detection. Our comprehensive analysis of current genomic language models provides insight into the importance of training data selection relative to model size, the need for domain-specific training, and the capabilities and limitations of genomic language models for detecting prophage sequences. This benchmark represents a challenging genomic annotation task in the bacterial domain and addresses a key computational problem with direct relevance to microbiology and medicine.

Prophages↗
PubMed2026

LAMBDA: A Prophage Detection Benchmark for Genomic Language Models.

Transformer-based genomic sequence models represent an emerging frontier in computational biology. Yet, their embeddings have not yet shown the same level of predictive power as natural and protein language models, indicating a gap between current implementations and theoretical promise. Existing benchmarks for DNA language models primarily focus on classifying regulatory elements in eukaryotic genomes, leaving open the fundamental question of whether these models learn sequence-level features across whole genomes. We introduce LAMBDA, a benchmark designed to rigorously evaluate genome language model embeddings through phage-bacteria sequence discrimination across four categories of increasing complexity: probing tasks, fine-tuning assessments, diagnostic tests, and genome-wide prophage detection. Our comprehensive analysis of current genomic language models provides novel insights into the importance of training data quality relative to model size, the need for domain-specific training, and the application of genomic language models for detecting prophage sequences. This benchmark represents a challenging genomic annotation task in the bacterial domain and addresses a key computational problem with direct relevance to microbiology and medicine.

DNA language model↗
PubMed1990

Isolation and characterization of DNA probes for human chromosome 21.

A coordinated effort to map and sequence the human genome has recently become a national priority. Chromosome 21, the smallest human chromosome accounting for less than 2% of the human genome, is an attractive model system for developing and evaluating genome mapping technology. Several strategies are currently being explored including the development of chromosome 21 libraries from somatic cell hybrids as reported here, the cloning of chromosome 21 in yeast artificial chromosomes (McCormick et al., 1989b), and the construction of chromosome 21 libraries using chromosome flow-sorting techniques (Fuscoe et al., 1989). This report describes the approaches used to identify DNA probes that are useful for mapping chromosome 21. Probes were successfully isolated from both phage and cosmid libraries made from two somatic cell hybrids that contain human chromosome 21 as the only human chromosome. The 15 cosmid clones from the WA17 library, reduced to cloned DNA sequences of an average size of 3 kb, total 525 kb of DNA which is approximately 1% of chromosome 21. From these clones, a set of polymorphic DNA markers that span the length of the long arm of chromosome 21 has been generated. All of the probes thus far analyzed from the WA17 libraries have been mapped to chromosome 21 both by physical and genetic mapping methods. It is therefore likely that the WA17 hybrid cell line contains human chromosome 21 as the only human component, in agreement with cytogenetic observation. The 153E7b cosmid libraries will provide an alternative source of cloned chromosome 21 DNA. Library screening techniques can be employed to obtain cloned DNA sequences from the same genetic loci of the two different chromosome 21s. Comparative analysis will allow direct estimation of DNA sequence variation for different regions of chromosome 21. Mapped DNA probes make possible the molecular analysis of chromosome 21 at a level of resolution not achievable by classical cytogenetic techniques (Graw et al., 1988; Van Keuren et al., 1989). Methods based on using region-specific chromosome 21 DNA probes and fluorescence in situ hybridization show promise for the rapid diagnosis of trisomy 21 (Lichter et al., 1988). The continued development of chromosome 21 DNA probes and advances in the technology of molecular cytogenetics will facilitate the study of the genetic organization of chromosome 21 and its role in the pathogenesis of Down syndrome.

Chromosomes, Human, Pair 21↗
PubMed2026

Whole exome sequencing identifies three novel variants and establishes the molecular diagnosis of ATP6V0A4-related distal renal tubular acidosis in a lebanese infant.

BACKGROUND: Distal renal tubular acidosis (dRTA) is a rare inherited disorder characterized by impaired urinary acidification, leading to metabolic acidosis, hypokalemia, nephrocalcinosis, and growth impairment. Pathogenic variants in ATP6V0A4 are among the most common genetic causes of autosomal recessive dRTA. METHODS AND RESULTS: We report a Lebanese infant presenting with failure to thrive, recurrent vomiting, severe hyperchloremic metabolic acidosis, hypokalemia, and bilateral nephrocalcinosis, in whom whole-exome sequencing (WES) was performed to establish the molecular diagnosis and perform a comprehensive genomic evaluation. WES identified three novel variants, including a novel homozygous likely pathogenic ATP6V0A4 variant, consistent with the patient's phenotype. Two additional novel variants in TTN and CEP290 were also detected. Family segregation analysis confirmed the inheritance pattern of all three variants and refined the interpretation of the additional genomic findings. The patient showed sustained clinical and biochemical improvement to alkali therapy, with normalization of biochemical abnormalities and improvement in growth during follow-up. CONCLUSIONS: This report expands the molecular spectrum of ATP6V0A4-related dRTA and illustrates the clinical utility of comprehensive WES combined with segregation analysis for accurate molecular diagnosis, variant interpretation, genetic counseling, and the evaluation of additional genomic findings in rare inherited disorders.

Humans↗
PubMed2026

Forty years in the field: reproductive biotechnologies shaping genetic progress in cattle in France.

Over the past four decades, reproductive biotechnologies have profoundly transformed cattle breeding by accelerating genetic progress and enabling the dissemination of elite genetics. In this article, I present a perspective based on more than 40 years of practical experience in embryo technologies within Auriva-Elevage, a cooperative organization serving 30,000 farmers in southern France. The development of embryo transfer in France was closely linked to genetic and sanitary challenges, particularly the introduction of North American Holstein genetics and the restrictions on live animal imports due to infectious diseases such as Infectious Bovine Rhinotracheitis. These constraints stimulated the development of national expertise in embryo transfer. Over the years, our team has implemented and adapted a wide range of reproductive technologies including in vivo embryo production and embryo transfer, cryopreservation, embryo sexing, ovum pick-up (OPU), in vitro embryo production (IVP), embryo biopsy, genomic evaluation of embryos, and laser-assisted biopsy techniques. The genomic revolution dramatically increased the strategic value of OPU-IVP for the rapid multiplication of elite donor females. In addition to technological developments, the success of these programs has depended heavily on internal training, collaboration with national organizations such as ELIANCE (previously UNCEIA, ALLICE) and research institutes including INRAE and Toulouse veterinary school, as well as strong international exchanges through scientific networks. Practical examples such as the use of embryo biopsy to prevent genetic diseases demonstrate the applied value of these technologies in breeding programs. This review highlights the technical evolution, organizational structures, and human expertise that have shaped the implementation of reproductive biotechnologies in cattle breeding and discusses the importance of anticipating future needs to ensure continued genetic progress.

OPU-IVP↗
PubMed2026

SpacerScope: binary-vectorized, genome-wide off-target profiling for RNA-guided nucleases without prior candidate-site bias.

The precision of CRISPR/Cas systems is fundamental to their application in plant and animal biotechnology. However, comprehensive sequence-based off-target candidate discovery remains a computational bottleneck, particularly in large and complex genomes. Here we developed SpacerScope, an off-target candidate discovery framework that enables unbiased, genome-wide discovery by leveraging binary vectorization, bitwise filtering, and right-end-anchored alignment. Benchmarking against human CIRCLE-seq data demonstrated that SpacerScope recovered 100% of validated off-target sites (6142/6142), matching the sensitivity of exhaustive algorithms. Crucially, SpacerScope achieved this maximum candidate recovery while substantially reducing computational overhead. In large-genome evaluations, SpacerScope maintained low peak memory usage of 2.20 GiB and achieved substantial runtime improvements over indel-aware comparator tools, including more than 50-fold speedup relative to Cas-OFFinder 3 (544 s versus 29 185 s). Furthermore, comparative analyses in polyploid species, such as the octoploid strawberry, revealed that SpacerScope identified larger sequence-compatible candidate burdens than standard web-based design platforms. Our results establish SpacerScope as a high-speed framework for sequence-based genome-wide off-target candidate discovery across diverse and highly repetitive genomic landscapes. The source code and program was publicly available at https://github.com/charlesqu666/SpacerScope. Short Abstract CRISPR/Cas sequence-based off-target candidate discovery remains computationally challenging in large, repetitive, and polyploid genomes. Existing tools either miss indel-containing candidate sites or incur prohibitive runtime and memory costs. We developed SpacerScope, a binary-vectorized framework that enables unbiased, genome-wide off-target candidate discovery without pre-selected candidate sites. By integrating bitwise filtering with right-end-anchored alignment, SpacerScope recovered 100% of validated off-target sites in human CIRCLE-seq data while using only 2.20 GiB of memory and achieving more than 10-fold speedup over indel-aware alternatives. Evaluation in plant genomes, including rice and octoploid strawberry, further demonstrated SpacerScope's capacity to identify larger sequence-compatible candidate burdens overlooked by standard tools. SpacerScope thus provides a high-speed framework for sequence-based genome-wide off-target candidate discovery across diverse and highly repetitive genomic landscapes, supporting downstream prioritization.

CRISPR-Cas Systems↗
PubMed2026

Assessment of genomic prediction and genetic gain in multi‑population half-sib families in the perennial grass crop intermediate wheatgrass.

The University of Minnesota has been domesticating the perennial forage intermediate wheatgrass (IWG) since 2011 using a combination of conventional methods and modern breeding tools such as genomic selection. Globally, most IWG selection nurseries are spaced-planted individuals of several hundred genotypes whereas commercial fields established for grain production are row-planted panmictic populations. This study evaluated genomic prediction models and estimated genetic gain in yield and agronomic performance of row-planted IWG half-sib families assessed over 3 years and 2 locations, Lamberton and St. Paul, MN, USA. The strongest trait correlation was negative (r = -0.49) between 2023 St. Paul height and 2022 St. Paul seed size. The three St. Paul environments were more similar for plant height and seed size and so were the Lamberton environments yet no specific trend was observed for grain yield. Evaluation of different univariate and multivariate genomic prediction models showed that multivariate models outperformed the best univariate models by 23 percentage points, yet no single multivariate model was the best predictor of all traits. Cross-environment predictions were the best among St. Paul environments and no single environment was the best predictor of the remaining environments. Genetic gain estimates indicated a 20 kg ha-1 increase in grain yield and 3 cm reduction in plant height per breeding cycle. While no single model predicted all traits with high accuracy, results obtained in this study suggest that evaluating IWG sibs in row plots followed by genomic trait predictions could lead to desired breeding progress for desired traits.

Poaceae↗
PubMed1998

Genetic imbalances in 67 synovial sarcomas evaluated by comparative genomic hybridization.

We used comparative genomic hybridization (CGH) to evaluate DNA sequence copy number changes in 67 synovial sarcomas of both monophasic and biphasic histological subtypes. Changes (mean among aberrant cases: 4.7 aberrations/tumor; range: 1-17), affecting most often entire chromosomes or chromosome arms, were detected in 37 sarcomas (55%). Gains and losses were distributed equally, but different chromosomes were affected with variable frequencies. The most frequent aberrations, each detected in 9-11 of 67 tumors, were gain of 8q and gain at 12q (12q14-15 and 12q23-qter), loss of 13q21-31, and loss of 3p. Other frequent changes (in 7 or 8 cases) included gains at 2p, 1q24-31, and 17q22-qter, and losses at 3cen-q23 and 10q21. High-level amplifications were seen in 7 cases. A total of 16 regions were detected. Two of them, 8p12-qter and 21q21-qter, seen in 4 and 2 tumors, respectively, were recurrent. No aberrations specific to histological subtype were identified. However, genetic changes in the monophasic tumors were more complex and numerous (mean among aberrant cases: 5.3 aberrations/tumor; range: 1-17) than in the biphasic tumors (mean: 2.5 aberrations/tumor; range: 1-5), and high-level amplifications occurred more frequently. All but 1 of the sarcomas showing high-level amplification were of the monophasic subtype. These findings may reflect differences in the pathogenesis and biological behavior of both histological subtypes of synovial sarcoma.

Adolescent↗
PubMed2002

Use of RNA and genomic DNA references for inferred comparisons in DNA microarray analyses.

In most microarray assays, labeled cDNA molecules derived from reference and query RNA samples are co-hybridized to probes arrayed on a glass surface. Gene expression profiles are then calculated for each gene based on the relative hybridization intensities measured between the two samples. The most commonly used reference samples are typically isolates from a single representative RNA source (RNA-0) or pooled mixtures of RNA derived from a plurality of sources (RNA-p). Genomic DNA offers an alternative reference nucleic acid with a number of potential advantages, including stability, reproducibility, and a potentially uniform representation of all genes, as each unique gene should have equal representation in a haploid genome. Using hydrogen peroxide-treated Arabidopsis thaliana plants as a model, we evaluated genomic DNA and RNA-p as reference samples and compared expression levels inferred through the reference relative to unexposed plants with expression levels measured directly using an RNA-0 reference. Our analysis demonstrates that while genomic DNA can serve as a reasonable reference source for microarray assays, a much greater correlation with direct measurements can be achieved using an RNA-based reference sample.

Arabidopsis↗
PubMedDate not supplied

Preliminary evaluation of prostate cancer metastatic risk biomarkers.

Prostate cancer patients at high risk of metastasis need to be identified as early as possible since metastasis is invariably fatal. Treatment could be tailored to risk. Recent array comparative genomic hybridization (aCGH) studies of primary and metastatic prostate tumors identified 39 BAC clones capable of detecting genomic signatures of metastasis. We termed these loci the genomic evaluators of metastatic CaP (GEMCaP). Risk assessments were made on a set of men who were managed with radical prostatectomy. We compared the utility of GEMCaP loci and the Kattan nomogram, a common risk assessment tool, in relation to biochemical outcome. This preliminary evaluation experiment suggests we can use aCGH to detect genomic signatures of metastasis in primary tumors with an accuracy of 78%. The classification accuracy for the Kattan nomogram was 75%. Therefore, validation of GEMCaP is warranted in a larger, appropriately designed cohort.

Biomarkers, Tumor↗
PubMed2002

Bioinformatics, functional genomics, and proteomics study of Bacillus sp.

The ability of bioinformatics to characterize genomic and proteomic sequences from bacteria Bacillus sp. for prediction of genes and proteins has been evaluated. Genomics coupling with proteomics, which is relied on integration of the significant advances recently achieved in two-dimensional (2-D) electrophoretic separation of proteins and mass spectrometry (MS), are now important and high throughput techniques for qualifying and analyzing gene and protein expression, discovering new gene or protein products, and understanding of gene and protein functions including post-genomic study. In addition, the bioinformatics of Bacillus sp. is embraced into many databases that will facilitate to rapidly search the information of Bacillus sp. in both genomics and proteomics. It is also possible to highlight sites for post-translational modifications based on the specific protein sequence motifs that play important roles in the structure, activity and compartmentalization of proteins. Moreover, the secreted proteins from Bacillus sp. are interesting and widely used in many applications especially biomedical applications that are the highly advantages for their potential therapeutic values.

Bacillus↗
PubMed2004

Outer breast quadrants demonstrate increased levels of genomic instability.

BACKGROUND: Theory holds that the upper outer quadrant of the breast develops more malignancies because of increased tissue volume. This study evaluated genomic patterns of loss of heterozygosity (LOH) and allelic imbalance (AI) in non-neoplastic tissues from quadrants of diseased breasts following mastectomy to characterize relationships between genomic instability and the propensity for tumor development. METHODS: Tissues from breast quadrants were collected from 21 patients with various stages of breast carcinoma. DNA was isolated from non-neoplastic tissues using standard methods and 26 chromosomal regions commonly deleted in breast cancer were examined to assess genomic instability. RESULTS: Genomic instability was observed in breast quadrants from patients with ductal carcinomas in situ and advanced carcinomas. Levels of instability by quadrant were not predictive of primary tumor location (P =.363), but outer quadrants demonstrated significantly higher levels of genomic instability than did inner quadrants (P =.017). Marker D8S511 on chromosome 8p22-21.3, one of the most frequently altered chromosomal regions in breast cancer, showed a significantly higher level of instability (P =.039) in outer compared with inner quadrants. CONCLUSIONS: Non-neoplastic breast tissues often harbor genetic changes that can be important to understanding the local breast environment within which cancer develops. Greater genomic instability in outer quadrants can partially explain the propensity for breast cancers to develop there, rather than simple volume-related concepts. Patterns of field cancerization in the breast appear to be complex and are not a simple function of distance from a developing tumor.

Breast↗
PubMed2006

Genome size and ploidy of Paracoccidioides brasiliensis reveals a haploid DNA content: flow cytometry and GP43 sequence analysis.

The aim of this study was to evaluate genome size and ploidy of the dimorphic pathogenic fungus Paracoccidioides brasiliensis. The cell cycle analysis of 10 P. brasiliensis isolates by flow cytometry (FCM) revealed a genome size ranging from 26.3+/-0.1Mb (26.9+/-0.1fg) to 35.5+/-0.2Mb (36.3+/-0.2fg) per uninucleated yeast cell. The DNA content of conidia from P. brasiliensis ATCC 60855-30.2+/-0.8Mb (30.9+/-0.8fg) -showed no significant differences with the yeast form, possibly excluding the occurrence of ploidy shift during morphogenesis. The ploidy of several P. brasiliensis isolates was assessed by comparing genome sizing by FCM with the previously described average haploid size obtained from electrophoretic karyotyping. The analysis of intra-individual variability of a highly polymorphic P. brasiliensis gene, GP43, indicated that only one allele seems to be present. Overall, the results showed that all analysed isolates presented a haploid, or at least aneuploid, DNA content and no association was detected between genome size/ploidy and the clinical-epidemiological features of the studied isolates. This work provides new knowledge on P. brasiliensis genetics/genomics, important for future research in basic cellular/molecular mechanisms and for the development/design of molecular techniques in this fungus.

Antigens, Fungal↗
PubMed2006

Extensive and genome-wide changes in the transcription profile of Staphylococcus aureus induced by modulating the transcription of the cell wall synthesis gene murF.

A murF conditional mutant was used to evaluate the effect of suboptimal transcription of this gene on the transcriptome of the methicillin-resistant Staphylococcus aureus strain COL. The mutant was grown in the presence of optimal and suboptimal concentrations of the inducer, and the relative levels of transcription of genes were evaluated genome wide with an Affymetrix DNA microarray that included all open reading frames (ORFs) as well as intergenic sequences derived from four sequenced S. aureus strains. Using a sensitivity threshold value of 1.5, suboptimal expression of murF altered the transcription of a surprisingly large number of genes, i.e., 668 out of the 2,740 ORFs (close to one-fourth of all ORFs), of the genome of S. aureus strain COL. The genes with altered transcription were distributed evenly around the S. aureus chromosome, and groups of genes involved with distinct metabolic functions responded in unique and operon-specific manners to modulation in murF transcription. For instance, all genes belonging to the isd operon and all but 2 of the 35 genes of prophage L54a were down-regulated, whereas all but one of the 21 members of the vraSR regulon and most of the 79 virulence-related genes (those for fibronectin binding proteins A and B, clumping factor A, gamma hemolysin, enterotoxin B, etc.) were up-regulated in cells with suboptimal expression of murF. Most importantly, the majority of these altered gene expression profiles were reversible by resupplying the optimal concentration of IPTG (isopropyl-beta-D-thiogalactopyranoside) to the culture. The observations suggest the coordinate regulation of a large sector of the S. aureus transcriptome in response to a disturbance in cell wall synthesis.

Bacterial Proteins↗
PubMed2025

Engineered Lactiplantibacillus plantarum and Levilactobacillus brevis utilizing ribonucleoprotein-mediated editing for inactivation of hemolysin gene.

Lactiplantibacillus plantarum and Levilactobacillus brevis are widely used probiotics with significant potential as chassis organisms for probiotic engineering. However, their bioengineering remains underdeveloped compared to that of other probiotic bacteria due to the limited availability of genetic tools. Although CRISPR-Cas systems have shown promise for genome editing in Lactobacillus species, strain- or site-specific targeting challenges must be overcome to enhance their broader applicability. This study aimed to develop a novel editing system with reduced dependency on plasmids and antibiotics in L. plantarum WCFS1, L. plantarum SPC 72 - 1 and L. brevis SPC-SNU 70 - 2 using a Cas9-gRNA ribonucleoprotein (RNP) complex. Although the hlyIII gene has been annotated as a hemolysin-related gene in several Lactobacillus genomes, no functional hemolytic activity has been definitively demonstrated to date. In this study, hlyIII was selected as a target to evaluate genome editing efficiency and to assess its potential relevance to strain safety. To construct ΔhlyIII strains, the RNP complex targeting hlyIII was separately transformed with recombinase RecE/T and double-stranded donor DNA. As a result, ΔhlyIII mutants were obtained under optimized electroporation conditions. Sequencing analysis revealed a 50 bp deletion and the introduction of a stop codon in hlyIII across all mutant strains. The hemolytic activity test showed a reduction in free hemoglobin levels in the ΔhlyIII strains compared to the wild type: 27.0%, 74.3%, and 5.0% in L. plantarum WCFS1, L. plantarum SPC 72 - 1, and L. brevis SPC-SNU 70 - 2, respectively. These results suggest strain-dependent differences in hemolytic activity and indicate that inactivation of hlyIII may contribute to reduced hemolysis, although further validation is needed to clarify its functional role. In conclusion, the hlyIII gene was successfully edited in L. plantarum and L. brevis using Cas9-gRNA ribonucleoprotein-mediated editing, demonstrating the feasibility of this genome editing platform for application in probiotic strains.

Gene Editing↗
PubMed1986

Identification of a second mutation in the protein-coding sequence of the Z type alpha 1-antitrypsin gene.

This study reports the entire nucleotide sequence of the protein coding region sequence of the alpha 1-antitrypsin (alpha 1AT) Z gene, a common form of the alpha 1AT gene associated with serum alpha 1AT deficiency. In addition to Glu342 to Lys342 mutation in exon V which has been previously identified by peptide analysis, another point mutation (GTG to GCG in exon III) in the gene sequence predicts a second amino acid substitution (Val213 to Ala213) in the Z protein. This Val213 to Ala213 mutation was confirmed to be a general finding in Z type alpha 1AT gene by evaluating genomic DNA from 40 Z haplotypes using synthetic oligonucleotide gene probes directed toward the mutated exon III sequences in the Z gene. Furthermore, the exon III Val213 to Ala213 mutation eliminates a BstEII restriction endonuclease site in the alpha 1AT Z gene, allowing rapid identification of this Val213 to Ala213 substitution at the genomic DNA level. Surprisingly, when genomic DNA samples from individuals thought to be homozygous for the M1 gene (the most common alpha 1AT normal haplotype) were evaluated with BstEII, 23% of the M1 haplotypes were BstEII site negative, thus identifying a new form of M1 (i.e. M1(Ala213], likely identical to M1 but with an isoelectric focusing "silent" amino acid substitution (Val213 to Ala213). Although the relative importance of the newly identified exon III Val213 to Ala213 mutation to the pathogenesis of the abnormalities associated with the Z gene is not known, it is likely that M1(Ala213) gene represents a common "normal" polymorphism of the alpha 1AT gene that served as an evolutionary intermediate between the M1(Val213) and Z genes.

Base Sequence↗