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PubMed1997

Evidence of genetic diversity underlying Rh D-, weak D (Du), and partial D phenotypes as determined by multiplex polymerase chain reaction analysis of the RHD gene.

The human blood group Rh antigens are expressed by proteins encoded by a pair of highly homologous genes located at chromosome 1p34-36. One of the genes (RHCE) encodes Rh CcEe antigens, while the other (RHD) the D antigen. Point mutations in the RHCE gene generate the C/c and E/e polymorphisms, while it has been shown that an RHD gene deletion can generate the D-negative phenotype. We have analyzed intron 4 of the RHCE and RHD genes and have defined the site of an RHD-specific deletion located in this intron. Using a multiplex RHD typing assay, which combines a reverse polymerase chain reaction (PCR) primer, which straddles this RHD-specific sequence, and a pair of primers located in exon 10 of the RHD gene, we have analyzed 357 different genomic DNA samples derived from individuals expressing D+, D-, weak D, and partial D phenotypes. Of these, we have noted a significant discordance with our multiplex PCR assay in the D- phenotypes dCcee and dccEe (which have been previously described) and weak D phenotypes. Our results suggest that in five serologically D- individuals we have identified an apparently intact RHD gene. Sequence analysis of transcripts obtained from one of these individuals (of phenotype dCCee) illustrates the presence of full-length RHD transcripts, which have a point mutation at nucleotide 121 (C --> T), which generates an in-frame stop codon (Gln41Stop). Thus, we describe a different molecular basis for generating the D- phenotype to the complete RHD gene deletion described previously. We also show that there are discordances with serotype and the multiplex assay in weak D and partial D phenotypes, indicating that the underlying molecular basis can be heterogeneous. Existing Rh D PCR assays assume the complete absence of the RHD gene in D- phenotypes. We describe a different molecular basis for generating the D- phenotype to the complete RHD gene deletion described previously.

Amino Acid Sequence↗

PubMed1997

Phenotypic variations and switches in HIV isolated from the blood and the gastrointestinal tissues of patients with HIV-1 infection. HIV/GI Research Study Group.

The objective of this study was to determine the initial and subsequent phenotypes of HIV-1 isolated from the blood, duodenal, and colonic biopsies of 51 HIV-1 positive patients followed prospectively over 2 years. Blood and tissues were cocultured with stimulated peripheral blood monocytes, and HIV was analyzed for phenotypic expression of syncytia-induction (SI). A total of 45/51 patients had HIV-1 isolated from the blood and 35/51 had HIV isolated from gastrointestinal tract. In 12/45 patients SI-HIV-1 was isolated from the blood. In 6/12 patients the blood phenotype reverted to the NSI phenotype. SI phenotypes were also isolated from the colon and duodenum of 8/35 patients and reversion from SI to NSI virus phenotype was again observed in gut tissue of 3/8 patients. These results show that gastrointestinal tissues can harbor SI HIV phenotype. Discordant phenotypes can be found in tissue and blood of late-stage patients. Reversion of phenotypic SI expression to NSI may occur in patients receiving monotherapy as antiretroviral treatment. These results suggest that gastrointestinal tissues may act as a separate and distinct site involved in HIV replication and its associated pathogenesis.

Biopsy↗

PubMed1998

Different alleles cause an imbalance in A2 and A2B phenotypes of the ABO blood group.

BACKGROUND AND OBJECTIVES: In several populations, including the Japanese, the frequency of the A2B phenotype is significantly higher than expected based on the A2 phenotype frequency. To understand the genetic basis of this 'excess' of A2B, we examined ABO alleles in individuals with A2-related phenotypes. MATERIALS AND METHODS: ABO alleles were identified by means of polymerase chain reaction single-strand conformation polymorphism (SSCP) and nucleotide sequence analyses. RESULTS: The frequencies of A2-related alleles (*A105, *A106, *A107, *A111 and *R101) were clearly different between the A2 and A2B phenotypes. In particular, a putative recombinant allele, *R101, was uncommon in the A2 but common in the A2B phenotype individuals. This allele was also detected in 4 of 401 (1%) unrelated A1 phenotype (AO genotype) individuals. CONCLUSION: *R101 is presumably expressed as phenotype A1 in *R101/*O heterozygous individuals, but as phenotype A2 in *R101/*B heterozygotes, thus giving rise to a high A2B phenotype frequency.

ABO Blood-Group System↗

PubMedDate not supplied

Histologic phenotypes of colonic carcinoma in Sweden and in Japan.

The occurrence of predominant histologic phenotypes in overt colonic carcinomas from two disparate geographical regions were analyzed. A total of 424 overt colonic carcinomas (223 in Swedish and 201 in Japanese patients) were classified into predominant phenotypes (i.e. comprising > 50% of the tumor). Six predominant phenotypes were found: tubular, serrated-microcystic, villous, fenestrated, signet ring cell and undifferentiated. A predominant phenotype was present in 57.3% (n = 243) of the 424 tumors (in 55.2% of the 223 tumors from Swedish patients and in 61.7% of the 201 tumors from Japanese patients). The serrated-microglandular phenotype was significantly more frequent in Japanese than in Swedish patients. Environmental and/or ethnic factors may be the possible cause(s) for that difference. The frequency of regional lymph node tumor spread (Dukes C) was significantly lower in serrated-microglandular and in villous phenotypes than in undifferentiated-signet ring cell types, despite that patients harbouring either one of the two former phenotypes were among the oldest in the whole series. Serrated-microglandular and villous colonic cancer phenotypes may carry a better prognosis (independently of their degree of histologic differentiation or age) since they are less prone to metastasize to regional lymph nodes than undifferentiated-signet ring cell phenotypes.

Adult↗

PubMed2002

Incidence of phenotypic aberrations in a series of 467 patients with B chronic lymphoproliferative disorders: basis for the design of specific four-color stainings to be used for minimal residual disease investigation.

Multiparameter immunophenotypic analysis of neoplastic cells has proven to be of great help for the investigation of minimal residual disease in acute leukemias; however, its utility has not been systematically explored in B cell chronic lymphoproliferative disorders. The aim of the present study was to investigate the incidence of phenotypic aberrations in a series of 467 consecutive leukemic B cell chronic lymphoproliferative disorders through the comparison of the phenotypic characteristics of tumor vs normal peripheral blood (n = 10) and bone marrow (n = 10) B cells, in order to explore the applicability of this strategy for minimal residual disease monitoring. An additional goal of our study was to evaluate the sensitivity of multiparameter flow cytometry for the detection of minimal residual disease in leukemic B cell chronic lymphoproliferative disorders through dilutional experiments (n = 19). From the patients analyzed 382 corresponded to B cell chronic lymphocytic leukemia/small lymphocytic lymphoma (353 typical and 29 atypical); five to prolymphocytic leukemia; 13 to hairy cell leukemias; 12 to lymphoplasmacytic lymphomas; 14 to splenic marginal zone lymphomas; 22 were follicular lymphomas; and 19 mantle cell lymphomas. The following triple stainings were systematically applied to both normal and leukemic samples: FMC7/CD5/CD19, CD22/CD23/CD19, CD103/CD25/CD19, CD10/CD11c/CD19 and sIg/sIg(lambda)/CD19. Overall, 98% of the leukemic B cell chronic lymphoproliferative disorders cases displayed aberrant phenotypes at diagnosis with no significant differences being found between cases analyzed in peripheral blood vs bone marrow samples. The most common types of aberrant criteria detected included asynchronous antigen expression (92%) and antigen over-expression (54%); abnormally light scatter characteristics were found in 17% of the cases. Most of the cases studied (90%) displayed four or more phenotypic aberrations. Once patients were divided according to the different diagnostic subgroups, the overall incidence of aberrant phenotypes ranged from 79 to 80% among atypical B cell chronic lymphocytic leukemia/small lymphocytic lymphoma and prolymphocytic leukemia to 97% of follicular lymphoma and 100% of typical B cell chronic lymphocytic leukemia/small lymphocytic lymphoma, hairy cell leukemia, lymphoplasmacytic lymphomas, splenic marginal zone lymphomas and mantle cell lymphomas. Based on the aberrant phenotypes detected unique four-color stainings could be built for the specific identification of aberrant phenotypes. These include CD22/CD23/CD19/CD5 and sIg(kappa)/sIg(lambda)/CD19/CD5 for lymphocytic leukemia/small lymphocytic lymphoma and prolymphocytic leukemia, CD103/CD25 or CD22/CD19/CD11c for hairy cell leukemia, FMC7/CD22/CD19/CD103 and sIg(kappa)/sIg(lambda)/CD22/CD19 for splenic marginal zone lymphomas, CD22/CD23/CD19/CD10 for follicular lymphomas and CD10/CD22/CD19/CD5 for mantle cell lymphomas. Serial dilutional experiments showed that the sensitivity level of immunophenotyping ranges between 10(-4) and 10(-5). In summary, the present study shows that immunophenotypic analysis allows the identification of aberrant phenotypes in 98% of leukemic B cell chronic lymphoproliferative disorders and these phenotypes can be used for minimal residual disease monitoring with a sensitivity limit of 10(-4)-10(-5).

Antibodies, Monoclonal↗

PubMed1999

Studies on strong and weak killer phenotypes of wine yeasts: production, activity of toxin in must, and its effect in mixed culture fermentation.

Two different killer phenotypes were detected among K+ (killer) yeasts isolated from spontaneous wine fermentations using a plate bioassay. The two phenotypes differed in their degree of killer activity, and were designated as SK+(strong killer) and WK+(weak killer). Strains showing either phenotype were assayed for expression of killer activity under different growth conditions. Growth in must negatively affected expression of the killer activity of both phenotypes. The supernatant fluids from must cultures showed a lower killing effect than those from yeast phosphate dextrose broth (YPDB) cultures. The ability of the two K+ phenotypes to prevail on K-sensitive yeasts was studied in mixed-culture fermentation experiments. Under these conditions, only strains showing SK+ phenotype were able to prevail on the K-sensitive yeasts. These results suggest that the K+ phenotype could play a relevant role in spontaneous fermentations provided that the strain exhibits an SK+ phenotype, and that the latter phenotype should be preferred when selected K + strains are to be used as fermentation starters.

Journal Article↗

PubMed2026

Genomic insights into stroke recovery: cross-phenotype associations.

Stroke is a major cause of long-term disability with variable recovery. While clinical factors such as initial severity play a role, genetic factors are increasingly recognized as important contributors to stroke recovery. Genotype studies are generally focused on a single post-stroke behavioural domain, but some genes might relate to broad mechanisms of plasticity. This study therefore aimed to identify cross-phenotypic genetic variants associated across two or more stroke recovery domains. DNA from Stroke, Stress, Rehabilitation, and Genetics study participants was genotyped, resulting in 9 814 610 variants. In order to examine cross-phenotypic results, we first conducted genome-wide association studies on the six recovery domains: motor (grip force), cognition (Telephone Montreal Cognitive Assessment), depression (Patient Health Questionnaire-8), stress (Primary Care Post-Traumatic Stress Disorder Screen), functional status (Stroke Impact Scale-Activities of Daily Living), and disability (modified Rankin Scale 0-2 versus 3-6), some of which were tested longitudinally, yielding nine phenotypes. Models were adjusted for age, sex, initial severity (NIH Stroke Scale score), and ancestry. Cross-phenotype associations were identified by evaluating single nucleotide polymorphisms (SNPs) associated (P < 5e-5) with multiple phenotypes. To determine how these genetic variants may relate to biological mechanisms of recovery, we conducted gene enrichment analyses. Participants (n = 565, 59% male) had mild-moderate initial stroke severity (median acute NIH Stroke Scale score = 4). After accounting for the correlation structure among the nine phenotypes, we observed 319 cross-phenotypic SNPs, 3.45 times the expected number. Five of the cross-phenotypic SNPs were linked to genes relevant to neural development, function and plasticity, e.g. ERICH1 (rs11778883-C), FOX3 (rs55726768-G), LIFR-AS1 (rs76401391-T), RPS6KA2 (rs113518460-C) and TUBGCP2 (rs147150392-C), as were enrichments in RAB5-EEA1, CTNNA1-CTNNB1, CIN85-SH3GL2 and ELMO1-DOCK2 complexes. Multiple gene enrichments were found, e.g. Stroke Impact Scale-Activities of Daily Living and Patient Health Questionnaire 8 at 3 months were enriched for CREB phosphorylation, which is important for long-term potentiation. We identified cross-phenotypic SNPs associated with multiple behavioural domains of stroke recovery. Some of these genes encode, or regulate, druggable proteins. These genetic factors are not well captured by clinical or neuroimaging assessments and so provide a unique window into stroke recovery. These findings, if validated, suggest that some genes may be broadly important to stroke recovery.

GWAS↗

PubMed2005

Histogenetic phenotypes of B cells in posttransplant lymphoproliferative disorders by immunohistochemical analysis correlate with transplant type: solid organ vs hematopoietic stem cell transplantation.

We immunohistochemically defined the histogenesis of posttransplantation lymphoproliferative disorders (PTLDs; B-cell phenotype) occurring after allogeneic T cell-depleted hematopoietic stem cell transplantation (HSCT; n = 15) or solid organ transplantation (SOT; n = 11) to determine whether transplantation type or morphologic subtype of PTLD affected the histogenetic subtype. Immunohistochemical stains using histogenetic markers for germinal center (GC) B cells, late GC and post-GC B cells, and post-GC B cells were performed on paraffin-embedded samples. Morphologically, 14 cases were polymorphic; 12 were monomorphic. Histogenetic marker expression was as follows: 1 monomorphic case (4%), GC phenotype expressing bcl-6 and CD10; 17 cases (65%; polymorphic, 9; monomorphic, 8), late GC-early post-GC phenotype expressing MUM1/IRF4; 8 cases (31%; polymorphic, 5; monomorphic, 3), post-GC phenotype expressing MUM1/IRF4 and CD138 but not bcl-6. PTLD cases after HSCT more frequently were post-GC phenotype than after SOT (7/15 vs 1/11, respectively; P = .040) and were independent of morphologic subclassification. Results suggest that most PTLDs are late GC-early post-GC phenotype with a minor group of post-GC phenotype and rare cases of GC phenotype. Findings also suggest a correlation between histogenetic phenotype of B-cell PTLD and type of transplantation.

Adult↗

PubMed2002

Establishment of a rat long-term culture expressing the osteogenic phenotype: dependence on dexamethasone and FGF-2.

Rat stromal bone-marrow cells cultured in the presence of dexamethasone, ascorbic acid, beta-glycerophosphate, and fibroblast growth factor-2 (FGF-2) express the osteogenic phenotype (Pitaru et al., J. Bone Miner. Res. 8:919-929, 1993). The purpose of this study was to establish a long-term homogeneous culture expressing the osteogenic phenotype. The cultures were routinely passaged every 5 days in the absence or presence of either or both dexamethasone and FGF-2, and the cumulative doubling number and the expression of the osteogenic phenotype were determined. Cultures treated with dexamethasone (10(-7) M) ceased proliferation and only upon addition of FGF-2 (3 ng/ml) was a spontaneous immortalization achieved, as expressed by sustained proliferation for about 1 year, with a doubling time of 22 h and more than 300 doublings in 72 passages. Both FGF-2 and dexamethasone are required and act synergistically to maintain cell propagation, alkaline phosphatase expression, and osteocalcin secretion; however, protein content was FGF-2 dependent and the mineralization was dexamethasone dependent. Repetitive single-cell cloning tested the homogeneity and stability of the cells expressing the osteogenic phenotype in these long-term cultures. It was shown that 25% to 50% of subclones derived from clones with an osteogenic phenotype do not further express the osteogenic phenotype. In conclusion, we have established a spontaneously immortalized dexamethasone- and FGF-2-dependent rat stromal bone-marrow-derived long-term culture expressing the osteogenic phenotype. The cultures tend to lose the osteogenic phenotype, and dexamethasone supports the long-term preservation of the osteogenic phenotype.

Alkaline Phosphatase↗

PubMed2026

Osteoarthritis phenotypes: advancing precision medicine through clinical, structural, and molecular stratification.

PURPOSE: Osteoarthritis (OA) is now understood as a heterogeneous syndrome driven by diverse biological, biomechanical, metabolic, genetic, and molecular mechanisms. This variability explains differences in disease progression and treatment response, challenging the traditional "one-size-fits-all" approach. This review highlights OA phenotyping as a key step toward precision medicine, focusing on clinical, structural, and molecular classifications that inform individualized care. METHODS: A narrative review was conducted using a non-systematic search of major databases and Osteoarthritis Research Society International sources (2010-2026). Evidence was thematically synthesized across clinical, imaging, and molecular domains to characterize OA phenotypes and their potential relevance to precision medicine. RESULTS: Multiple OA phenotypes were identified: inflammatory, metabolic, biomechanical, cartilage-subchondral, pain-sensitization, and aging/senescence. These exhibit distinct clinical features, risk factors, and therapeutic responses. Imaging-based phenotypes (e.g., inflammatory, meniscus-cartilage, subchondral bone, atrophic, hypertrophic) and molecular endotypes (low turnover, structural damage, systemic inflammation) further refine stratification. Pain-structure discordance is notable in sensitization phenotypes and may predict poorer surgical outcomes. Joint-specific variations and emerging genomic and epigenetic insights underscore disease complexity. Advances in imaging, biomarkers, and machine learning may enable earlier detection and patient clustering, though clinical application remains limited. CONCLUSION: Phenotype- and endotype-based classification represents a critical advancement toward precision OA management. Tailored interventions based on stratification hold promise for improving outcomes; however, clinical translation remains limited by overlapping phenotypes, lack of validated biomarkers, and inconsistent results from phenotype-driven trials. Wider clinical adoption requires standardized definitions, validation across joints, and integration of multimodal diagnostic tools into routine practice.

Humans↗

PubMed2026

The bidirectional genetic causality between immunocyte phenotypes and dilated cardiomyopathy: A bidirectional Mendelian randomization study.

The association between immunocyte phenotypes and dilated cardiomyopathy (DCM) has been explored, however the exact pathogenesis of the relationship between immune cells and DCM is unclear. This bidirectional two-sample Mendelian randomization (MR) research aims to further validate the causal link between 731 immunocyte phenotypes and DCM. Summary statistics from a genome-wide association study data of individuals with European ancestry were utilized, including 1444 DCM cases and 353,937 controls, as well as 3757 European adults for the 731 immunocyte phenotypes. Causal effects were estimated using inverse variance weighted, MR-Egger regression, weight median estimator, weighted mode, and simple mode. Sensitivity analysis was conducted to confirm data robustness and feasibility. Based on the inverse variance weighted findings, 14 immunocyte phenotypes were risk factors for DCM (P < .05, odds ratio [OR] > 1), while 15 immunocyte phenotypes exhibited a protective effect on DCM (P < .05, OR < 1). The results of reverse MR analysis suggested evidence that DCM occurrence might elevate the levels of 17 immunocyte phenotypes (P < .05, OR > 1) and decrease the levels of 9 immunocyte phenotypes (P < .05, OR < 1). Our research indicated that CD28 on secreting regulatory T cell could mitigate the occurrence of DCM, and reciprocally, the progression of DCM could reduce the level of CD28 on secreting regulatory T cell. This study confirmed the bidirectional genetic predictive relationship between immunocyte phenotypes and DCM, underscoring the complex interplay between DCM and the immune system.

Cardiomyopathy, Dilated↗

PubMed2026

Phenotypes of Hereditary Diseases Associated With Rauch-Steindl Syndrome.

PURPOSE: Prenatal phenotypic manifestations of genetic disorders associated with NSD2 variants remain poorly characterized. This study presents our institutional experience with the prenatal diagnosis of NSD2-associated genetic disorders, specifically Rauch-Steindl syndrome (RAUST), aiming to improve understanding of both the molecular and clinical features of RAUST. METHODS: We performed a retrospective analysis of six fetuses and one adult diagnosed with RAUST at our institution and thoroughly reviewed the prenatal ultrasound reports of six fetuses. Prenatal and postnatal phenotypes of RAUST cases were summarized alongside findings from previously published literature. Correlations between NSD2 variant locations, variant types, and phenotypes were analyzed. Additionally, protein modeling was used to visualize structural changes in NSD2 protein before and after C-terminal variants. We integrated single-cell transcriptomic and gene expression data from multiple public databases to investigate spatiotemporal expression patterns of NSD2 during human fetal development. RESULTS: Fetal growth restriction (FGR) was the most prevalent prenatal manifestation in RAUST fetuses, followed by microcephaly. Bilateral renal hypoplasia emerged as a novel prenatal ultrasonographic feature. Postnatally, speech and motor developmental delays were the most commonly reported phenotypes, followed by physical developmental delays and intellectual disability. Genotype-phenotype correlation analysis revealed an association between N-terminal truncating variants in NSD2 and impaired fetal growth parameters. Notably, C-terminal truncating variants-predicted not to directly impact NSD2 functional domains-also exerted disease-causing effects. CONCLUSION: This study provides a comprehensive analysis of prenatal phenotypes in RAUST cases, enriching the prenatal phenotypic spectrum of the disease and facilitating early diagnosis and clinical management of RAUST. Furthermore, our genotype-phenotype correlation findings lay a foundational basis for future research into the complex molecular mechanisms underlying NSD2-associated genetic disorders.

Humans↗

PubMed2026

First-line drug-resistant tuberculosis among children under 15 years in Ethiopia: insights from phenotypic and whole-genome sequencing approaches.

BACKGROUND: Childhood drug-resistant tuberculosis is often underdiagnosed and inadequately characterized due to the paucibacillary nature of the disease. This study aimed to assess resistance to first-line anti-tuberculosis drugs in children using phenotypic drug susceptibility testing and whole-genome sequencing. METHODS: A retrospective-prospective study was conducted on culture-confirmed childhood tuberculosis cases in Ethiopia (2017–2023). Phenotypic drug susceptibility testing was performed on 110 Mycobacterium tuberculosis complex isolates. Whole-genome sequencing was completed for 85 of these isolates, which were analyzed using the TB-Profiler and MTBSeq pipelines. We assessed the sensitivity, specificity, predictive values, and kappa agreement of whole-genome sequencing compared with phenotypic drug susceptibility testing. RESULTS: Phenotypic resistance to at least one first-line anti-TB drug was observed in 26/110 (23.6%) of the examined isolates, with isoniazid resistance being the most frequent, 23/110 (20.9%), followed by rifampicin resistance, 18/110 (16.4%). TB-Profiler showed almost perfect agreement with phenotypic drug susceptibility testing for rifampicin (sensitivity 94.4%, kappa = 0.96) and isoniazid (sensitivity 91.3%, kappa = 0.91), whereas MTBSeq showed slightly lower performance. Both pipelines demonstrated moderate to weak agreement with phenotypic drug susceptibility testing for detecting resistance to ethambutol, pyrazinamide, and streptomycin. The most frequently observed resistance mutations among phenotypically resistant isolates were rpoB (Ser450Leu), katG (S315Thr), embB (Met306Ile), and pncA (C-11 A > G) for rifampicin, isoniazid, ethambutol, and pyrazinamide, respectively. Discrepancies between genotypic and phenotypic drug susceptibility testing were observed across all first-line anti-TB drug-resistant isolates, particularly for ethambutol and pyrazinamide. CONCLUSION: We found a high prevalence of isoniazid resistance, along with rifampicin resistance, underscoring the need for early detection in vulnerable groups. Whole-genome sequencing showed good accuracy for these drugs, with TB-Profiler performing best. CLINICAL TRIAL NUMBER: Not applicable.

Humans↗

PubMed1998

Phenotype 2 of deoxyribonuclease I may be used as a risk factor for gastric carcinoma.

BACKGROUND: Human deoxyribonuclease I (DNase I) (EC3.1.21.1) is one of the candidate nucleases that acts in mammalian cells during apoptosis. Genetic polymorphism of DNase I has been classified into 15 phenotypes controlled by 5 autosomal codominant alleles. The purpose of this study was to determine whether DNase I polymorphism is closely related to the incidence of gastric carcinoma. METHODS: The phenotype distribution was examined using urine samples obtained from unrelated Japanese patients with gastric carcinoma (n = 97) and benign gastric diseases (n = 76). Phenotyping was performed using isoelectric focusing electrophoresis in thin polyacrylamide gel and immunoblotting with an antihuman DNase I antibody. RESULTS: A close statistical association was found between patients with gastric carcinoma and a high frequency of DNase I phenotype 2. However, there was no significant difference in the phenotype distribution between the group of patients with benign gastric diseases and the controls. CONCLUSIONS: The findings of the current study suggest that DNase I phenotype 2 may be a marker for gastric carcinoma. Therefore, compared with other phenotypes, DNase I phenotype 2 may have potential for identifying patients who are at risk of harboring or developing gastric carcinoma.

Adult↗

PubMed1997

Modeling the phenotype in parametric linkage analysis of bipolar disorder.

The definition of phenotype is a major problem in genetic studies of psychiatric disorders. Most linkage studies in bipolar disorder have defined the phenotype as a dichotomous trait and have usually employed different hierarchical classifications in order to overcome uncertainty resulting from phenotypic variability. In this study we explored the advantages of maximizing the evidence for linkage over different phenotypic definitions when conducting parametric linkage analysis of a complex trait. The GAW10 Problem 1 was used, focusing on chromosome 18 data sets. Three major phenotypic models were analyzed: quasi-quantitative, liability-based and affection-status models. Overall, no single phenotypic model performed consistently better than the others (i.e., lod scores greater than 1.0). Each model yielded higher lod scores than the others in particular instances, suggesting that it might be useful in exploratory data analysis, where the phenotype is variable, to maximize evidence for linkage over different phenotypic models.

Bipolar Disorder↗

PubMed2004

Phenotypical variation in cousins with the identical partial trisomy 9 (pter-q22.2) and 7 (q35-qter) at 16 and 23 weeks gestation.

From the study of numerical and structural chromosomal abnormalities, there is convincing evidence and accumulating information of a direct karyotype to phenotype correlation. Knowledge of phenotypic consequences of a specific chromosomal imbalance is important for genetic counseling and prenatal diagnosis. However, for unbalanced non-Robertsonian translocations a precise karyotype to phenotype correlation is difficult to predict for several reasons: (I) unbalanced non-Robertsonian translocations are rare, (II) the published case reports are often not age-matched, (III) varying breakpoints result in different lengths of the monosomic and trisomic segments and therefore the phenotype will depend on additional genes present or the loss of coding regions, and (IV) the combination of the same trisomy with different monosomies, or vice versa, can result in diverging phenotypes. Therefore, the study of the karyotype to phenotype correlation in affected relatives of the same age and the identical unbalanced translocation provides a good model to investigate phenotypic consequences of a specific genetic imbalance. We report of two second trimester fetuses with the identical major partial trisomy 9 (9pter-9q22.2) and minor partial trisomy 7 (q35-qter) resulting from a familial translocation (7;9)(q35;q22.2)mat. One fetus presented with a Dandy-Walker malformation, polymicrogyria, and mild dysmorphic features, whereas the other fetus showed unilateral cleft lip and palate without cerebral anomalies. Potential mechanisms for this different phenotypic expression of the same unbalanced translocation resulting in partial trisomy 9 and 7 in the two cousins and possible consequences for genetic counseling and prenatal diagnosis are discussed.

Abnormalities, Multiple↗

PubMed2006

Phenotypic approaches for understanding patterns of intracemetery biological variation.

This paper reviews studies of phenotypic inheritance and microevolutionary processes in archaeological populations using data on cranial and dental phenotypic variation, often referred to as paleogenetics or biodistance analysis. The estimation of biological distances between populations, or among individuals within populations, is one component of bioarchaeological research on past populations. In this overview, five approaches that focus on morphological variation within cemeteries are summarized: kinship and cemetery structure analysis, postmarital residence analysis, sample aggregate phenotypic variability, temporal microchronology, and age-structured phenotypic variation. Previous research, theoretical justifications, and methods are outlined for each topic. Case studies are presented that illustrate these theoretical and methodological bases, as well as demonstrate the kinds of inferences possible using these approaches. Kinship and cemetery structure analysis seeks to identify the members of family groups within larger cemeteries or determine whether cemeteries were kin-structured. Analysis of sex-specific phenotypic variation allows estimation of postmarital residence practices, which is important for understanding other aspects of prehistoric social organization. Analysis of aggregate phenotypic variability can be used to infer site formation processes or cemetery catchment area. The study of temporal microchronologies can be used to evaluate provisional archaeological chronologies or study microevolutionary processes such as adaptive selection or changing patterns of gene flow. Finally, age-structured phenotypic variation can be reflective of selection processes within populations or it can be used as a measure of morbidity, growth arrest, and early mortality within past populations. Use of phenotypic data as a genotypic proxy is theoretically sound, even at small scales of analysis.

Adolescent↗

PubMed2026

Phenotypic and transcriptomic characterization of biallelic RNU2-2 developmental and epileptic encephalopathy.

OBJECTIVE: A significant proportion of individuals with suspected genetic developmental and epileptic encephalopathies (DEEs) remain unsolved following whole genome sequencing (WGS). Here we describe biallelic RNU2-2 variants causing a recently reported, severe, recessive DEE. METHODS: We screened individuals who have received WGS analyses at the Genomic Medicine Centre Karolinska for Rare Diseases for biallelic RNU2-2 variants. Deep phenotyping was performed through reviewing entire medical histories and phenotypic traits were transcribed to their corresponding Human Phenotype Ontology (HPO) term. HPO terms were used to generate pairwise phenotypic similarity scores and assess for significantly shared phenotype enrichment in the RNU2-2 sub-cohort. RNA sequencing analyses were performed in fibroblast and blood tissues to compare splicing events between RNU2-2 individuals and two independent control groups. RESULTS: We identified 14 individuals from nine families with 12 ultra-rare biallelic RNU2-2 variants clustering in the conserved 5' domains. Genotype data from 13 of 14 individuals has been reported previously as part of a larger cohort. All individuals presented with a highly concordant, severe DEE, characterized by severe to profound intellectual disability, inability to walk or communicate, hyperkinesia, and refractory seizures. Infantile spasms and tonic seizures were the predominant seizure types and a Lennox-Gastaut syndrome-like phenotype was common. These individuals had a significantly similar phenotypic signature when compared with 703 individuals with complex pediatric epilepsies (two-sided Monte Carlo permutation test, p = .005). RNA sequencing analyses showed aberrant splicing, with the most pronounced effects in fibroblast tissues in mutually exclusive exon and alternate 3' splice-site events, which were not detectable in blood. SIGNIFICANCE: We present deep phenotyping data and transcriptomic analyses that provide support for rare, 5' clustering biallelic RNU2-2 variants causing this novel, severe DEE. We propose an RNA sequencing methodology on fibroblast tissue for future validation of RNU2-2 variants.

autosomal recessive disease↗