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Serological detection and molecular localization of allelic HLA-DP supertypic epitopes.

A DP serological allospecificity was identified using 125I-labeled preparations of HLA class II molecules isolated from cells of HLA homozygous typing cell lines, SLE (DRw6, DQw1, DPw3) and WT46 (DRw6, DQw1, DPw2), and depleted of DR molecules by absorption with an anti-DR monoclonal antibody. The specificity, provisionally called WT, was carried by class II molecules possessing the characteristics of DP molecules on sodium dodecyl sulfate-polyacrylamide gel electrophoresis, and detected primarily in DPw1, DPw3 and DPw5 cells and exceptionally in some DPw2 cells including WT46 and DPw4 cells on a large panel of DP-pretyped B cell lines mostly derived from the 10th International Histocompatibility Workshop B cell reference panel. It was apparently allelic to another DP serological specificity BUT previously defined on DP molecules isolated from cells of DPw2+ HLA deletion mutant cell line LCL 721.82. On the same cell panel; the BUT specificity was negative in all DPw1, DPw3 and DPw5 cells, and positive in all DPw2 and DPw4 cells and also in DPw2B and DPw4B cells except the cells typed WT+. This DP association pattern was similar to that of the known allelic sequences, GGPM and DEAV, in DP beta F segment, one of the six variable segments in the second exon of DP beta gene. Thus, genomic DNA from 22 B cell lines pretyped for BUT and WT specificities were enzymatically amplified for the second exon of DP beta gene by the use of locus-specific oligonucleotide primers and hybridized with 32P-labeled oligonucleotide probes corresponding to the F segment sequence variations. This oligonucleotide typing showed perfect one-to-one correlation with the BUT and WT serological typing. The typing also revealed that WT46 cells, although typed DPw2, have the DEAV sequence common to DPw1, DPw3 and DPw5.

Alleles↗

Loci for efficient detection of microsatellite instability in hereditary non-polyposis colorectal cancer.

Most hereditary non-polyposis colorectal cancer (HNPCC) is due to germline mutations in DNA mismatch repair genes. Tumors arising as a result of these mutations display instability in microsatellites, which are short tandem repeats of DNA that are distributed throughout the genome. Although a subset of sporadic colorectal carcinomas also have microsatellite instability (MSI), the phenotype is a useful screening test in identifying patients with HNPCC caused by mutations in mismatch repair (MMR) genes. Studies have shown that some microsatellite markers are more efficient than others in identifying tumors with MSI. Furthermore, the frequency of instability can be assessed by categorizing patients into high (MSI-H, >/= 30-40% positive markers), low (MSI-L), and microsatellite stable (MSS) groups. Using a panel of 28 microsatellite markers, tumor and normal DNA from 10 HNPCC patients was used to identify the five most efficient markers for detecting MSI (BAT26, D2S123, FGA, D18S35, and TP53-DI). Each of the five markers detected MSI in 80-100% of the cases examined. We then expanded the sample size to 17 tumors from HNPCC patients. Each case had evidence for a mutation in either hMSH2 or hMLH1. We compared the efficiency of our panel of five best markers with another panel of five markers (BAT25, BAT26, D2S123, D17S250, and D5S346) identified as being efficient markers for detection of MSI at a recent NCI workshop. Our five selected markers were more efficient (85% vs. 79%) in detecting MSI. However, using either panel, 100% of the cases fell into the MSI-H category and the probability of misclassifying an MSI-H case as MSI-L is very low (0.002-0.008). We also examined four cases meeting the Amsterdam criteria for HNPCC, but with no evidence for mutation in either the hMSH2 or hMLH1 gene. With our panel, three were classified as MSI-H, while only two were classified as such with the NCI reference panel. The probability of misclassifying an MSI-L case as an MSI-H, using a panel of five markers is high (0.263).

Basic Helix-Loop-Helix Proteins↗

[A standard panel of human immunodeficiency virus-positive and -negative blood sera for assessing the sensitivity and specificity of diagnostic immunoenzyme test systems].

The materials on the development of a reference panel of HIV-positive and negative blood sera required for quality control of diagnostic enzyme-immunoassay systems are summarized. Ninety sera (50 HIV-antibody positive and 40 negative) were examined in 2 test systems of national and 3 test systems of foreign companies as well as by immune blotting and immunofluorescence tests. Each serum was characterized by optic density values and antibody titer (for positive sera). The conditions of storage and transportation of serum panels as well as those for control tests were determined. The license and instructions for use for the serum panel have been approved. The serum panel is used in 9 institutions engaged in working out and manufacture of diagnostic test systems.

AIDS Serodiagnosis↗

A serological screening assay of human immunodeficiency virus type 1 antibodies based on recombinant protein p24-gp41 as a fusion protein expressed in Escherichia coli.

The objective of this study was expression of a recombinant fusion protein p24-gp41 to gain a proper folding pattern of the proteins which could be recognized by specific antibodies against human immunodeficiency virus type 1 (HIV-1) for development of a reliable serodiagnostic kit. Serodiagnostic method using enzyme-linked immunosorbent assay (ELISA) with the expressed recombinant fusion protein p24-gp41 was carried out to test the sensitivity and specificity of the protein using human sera and various reference panels from Boston Biomedica Inc. (BBI). The level of the expression was determined to be 30% and the final recovery from fermentation and purification process was calculated as 80 mg/L with more than 98% purity. The developed ELISA assay was demonstrated to have 100 and 99.5% sensitivity and specificity, respectively, detecting anti-HIV-1 antibody using 900 positive and 10,000 negative human sera. The developed assay showed reliable results in comparison with other reference HIV ELISA kits using various BBI panels as well. In conclusion, the recombinant fusion protein p24-gp41 was expressed and used to develop a serodiagnostic kit for screening of the HIV-1 with high sensitivity (100%) and specificity (99.5%) which could be useful for screening large groups of blood donors.

Enzyme-Linked Immunosorbent Assay↗

Lack of evidence for association between the endothelial nitric oxide synthase gene and hypertension.

Significant association between a Glu298Asp polymorphism of the endothelial nitric oxide synthase (eNOS) gene and essential hypertension was recently reported in Japanese populations, with the 298Asp variant showing a higher prevalence in hypertensive patients (10.3% to 12.0%) than in normotensive subjects (5.0% to 5.8%). In contrast, another study demonstrated that the 298Glu variant was significantly associated with hypertension in a Caucasian population. We therefore undertook an extensive association study in Japanese to resolve these contradictory claims. A total of 1165 individuals were selected from clinic outpatients and hospital staff in a single institution. The relevance of the Glu298Asp polymorphism to hypertension in this population was tested in 2 ways. First, a case-control study was conducted in 549 hypertensive and 513 normotensive subjects within the study population, with the chi2 statistic used to test the significance of an association between eNOS genotype and the presence of hypertension. Second, an ANOVA was used to test the significance of an association between eNOS genotype and the level of blood pressure within the entire population except for 167 hypertensive subjects who had been under treatment for hypertension. No significant association was observed in either of the statistics tested. Allele frequencies of 298Asp were concordant across the panels: 8.4% in hypertensive subjects, 8. 2% in normotensive subjects, and 7.9% and 9.5% in 2 additional sample populations used as reference panels. Taken together, our results do not support the previous observation that the molecular variant of the eNOS gene may confer principal susceptibility for essential hypertension but rather suggest the existence of sampling variation.

Adult↗

Evaluation of PAPNET testing as an ancillary tool to clarify the status of the "atypical" cervical smear.

To assess the utility of the PAPNET system (Neuromedical Systems Inc., Suffern, NY) in clarifying the status of cervical smears showing borderline abnormalities, we analyzed the results of five cytotechnologists who reclassified 200 "atypical" smears by evaluating PAPNET images only. The interobserver agreement (reliability) of the PAPNET reviewers was computed, and their readings were compared with three standards: the consensus diagnosis of five pathologists who used light microscopy, the detection of cancer-associated human papillomavirus DNA by Southern analysis, and the correlation with diagnoses of biopsy specimens obtained during passive follow-up. The PAPNET reviewers classified 18 to 65% of cases as normal, 25 to 42% as equivocal, and 10 to 55% as abnormal. Unanimous interobserver agreement was achieved in only 24 (13%) cases. Four of the five PAPNET reviewers agreed moderately well with the results of the pathology reference panel. In four of the five PAPNET reviews, classification of cases as abnormal was strongly correlated with the detection of cancer-associated types of human papillomavirus. Consensus PAPNET results of abnormal were predictive of abnormal histologic findings at follow-up. Theoretically, if colposcopy had been performed on all of the women with equivocal or abnormal PAPNET results (based on the consensus of the panel), as much as 95% of biopsy-confirmed lesions could have been detected, but 79% of women would have been referred. Restriction of colposcopy referral to women with definitely abnormal PAPNET readings would have reduced referrals to 31%, but the sensitivity of the triage would have dropped to 51% of biopsy-confirmed lesions.

Biopsy↗

Office-based testing for antibody to human immunodeficiency virus in urology patients.

Knowledge of the status of a patient regarding antibody to human immunodeficiency virus type 1 (HIV-1) may be important in many clinical situations. Consequently, we evaluated a rapid test for antibody to HIV-1 peptides that might be suitable for a physician office practice. We evaluated the time necessary to learn to do the test, and test performance using a reference panel and a seroconversion panel as well as 200 clinical specimens. Personnel who were previously unfamiliar with immunoassays learned the test procedure within 30 minutes. All reference specimens were interpreted correctly. One clinical sample reacted in the test but the result was not confirmed by Western blot. The rapid, peptide-based test was easy to use and performance was comparable to currently licensed tests performed at clinical laboratories.

AIDS Serodiagnosis↗

Physical and linkage mapping of the bovine bone morphogenetic protein 1 on the evolutionary break region of BTA 8.

Bone morphogenetic protein 1 (BMP1) has been proposed as a regulatory molecule involved in the binding or activation of other BMP molecules. It has been described as being identical to the enzyme C-proteinase that processes procollagens to fibrillar collagens. A fragment containing an exon of the bovine BMP1 gene was amplified from an adapter-ligated genomic DNA library. The isolated bovine BMP1 fragment was assigned by fluorescence in situ hybridization (FISH) to bovine (BTA) chromosome 8q21, a region containing an evolutionary breakpoint between homology to human (HSA) chromosomes 8 and 9. The assignment to BTA 8 was confirmed by using a hybrid somatic cell panel. The 3' intron region of the amplified genomic BMP1 fragment showed a SSCP polymorphism, and linkage analysis in the International Bovine Reference Panel (IBRP) of families confirmed the boundary position of this gene. The BMP1 gene presents total linkage (theta = 0.00, Z = 3.61) with the lipoprotein lipase gene on BTA 8 and HSA 8 and a larger recombination fraction (theta = 0.11, Z = 5.03) with the marker GGTB2 on BTA 8 and HSA 9. Physical and genetic mapping of the bovine BMP1 gene contribute to narrow the boundary between the HSA 8 and HSA 9 homology segments on BTA 8 and to the comparative mapping between BTA 8, murine chromosome MMU 14, and HSA 8.

Animals↗

Natural antibody status in patients with Hashimoto's thyroiditis.

Raised levels of circulating natural antibodies (NABS) have been found in association with systemic lupus erythematosus (SLE) and chronic active hepatitis (CAH), indicative of polyclonal B-cell activation associated with these relatively non-organ specific autoimmune diseases. This study examined the natural antibody response in the organ-specific autoimmune disease Hashimoto's thyroiditis. Serum samples obtained from 69 women with newly diagnosed Hashimoto's thyroiditis together with 64 controls were analysed for IgG and IgM NABS directed at DNA, actin, myoglobin, myosin, trinitrophenyl hapten (TNP) and tubulin as the NAB antigen panel using an established ELISA. The same technique was also used to estimate thyroglobulin and thyroid microsomal autoantibody activities. Compared to a reference panel of normal serum samples, 31 of the Hashimoto's samples showed a greater than 2SD elevation of IgG and/or IgM NABS against one or more of the panel antigens together with elevated IgG thyroglobulin and thyroid microsomal antibody levels. The cases positive for one or more of the NAB panel also showed a greater incidence of active Hashimoto's thyroiditis as indicated by the presence of antibodies directed against the thyroid specific antigens. The above findings suggest that raised levels of NABS are also a feature of this organ-specific autoimmune disease. The wide ranging NAB specificities involved are consistent with an underlying or epiphenomenal state of polyclonal B-cell activation.

Antibodies, Antinuclear↗

Reference-Free Microsatellite Instability Detection from Tumor Sequencing Using Intrasample Variability Modeling.

Microsatellite instability (MSI) is a predictive biomarker in several tumor types. However, many next-generation sequencing-based callers require matched normal samples, reference panels, or pretrained models, limiting their portability across assays and sequencing centers. We developed PROMIS (PROfiling of Microsatellite InStability), a tumor-only, reference-free pipeline that uses a discrete mixture model to characterize intrasample repeat-length distributions at predefined microsatellite loci. Locus-level classifications are then aggregated into a continuous MSI score. We benchmarked PROMIS in colorectal (CRC), endometrial (UCEC), and gastric (STAD) cancers from The Cancer Genome Atlas. PROMIS achieved an overall area under the receiver operating characteristic curve (AUC) of 0.995 and cohort-specific AUCs of 1.00 in CRC and stomach adenocarcinoma and 0.999 in uterine corpus endometrial carcinoma, comparable to established tools despite not using matched normals or pretrained models. Subsampling demonstrated robust performance with substantially fewer loci. In silico dilution showed progressively reduced MSI-microsatellite-stable discrimination, with the pooled AUC declining from 0.83 at 10% tumor fraction to 0.53 at 1%. At low tumor fractions, tumor-type-specific baseline microsatellite variability increasingly influenced PROMIS scores. Finally, in prostate and CRC cell-free DNA cohorts, including Illumina TSO500 data and an 18-gene panel, PROMIS yielded MSI scores concordant with orthogonal tissue- and panel-based classifications across the evaluated Illumina-based sequencing contexts. Accordingly, the present validation should be considered limited to Illumina-based sequencing platforms. PROMIS is intended to complement existing genomic profiling workflows by enabling MSI assessment from sequencing data already generated for broader molecular analyses. Prospective clinical validation remains necessary before clinical implementation.

Journal Article↗

Diagnostic discord with melanoma.

The study of the Pathology Panel of the Dutch Melanoma Working Party highlights the great difficulty in achieving uniform diagnostic assessment of melanoma. Their solution is to set up a national reference panel and to focus continuing medical education on identified areas of particular difficulty. This could be appropriate for other countries, although selection of referees and funding may be problematic. It may also be timely to consider whether melanoma terminology can be rationalized to make it more likely to be reported consistently by pathologists whilst still providing sufficient information for proper patient management. Alternatively the reporting of most melanocytic lesions could be confined to pathologists who specialise in this subject, a practice which has evolved for other areas of pathology. This would facilitate the maintenance of standards and uniformity among that smaller group, but it would not avoid the need for a continuing awareness among all pathologists of the diagnostic pitfalls which abound in the area of melanocytic lesions.

Humans↗

Detection of microsatellite instability in endometrial cancer: advantages of a panel of five mononucleotide repeats over the National Cancer Institute panel of markers.

The aim of this study was to find the optimal set of microsatellite markers for diagnosis of the microsatellite instability (MSI) phenotype in endometrial cancers. We compared the sensitivity, specificity and ease of use of a reference panel of five markers originally recommended by the National Cancer Institute (NCI) for colorectal cancer and a panel of five quasi-monomorphic mononucleotide repeat markers (pentaplex PCR system). We used these panels for establishing the MSI status of a series of 80 sporadic endometrial adenocarcinomas by comparing the allelic profiles of the markers between tumor and matching germline DNA. Both panels detected the same subset of 21 out of 80 (26%) endometrial MSI carcinomas. However, in the MSI cases, the mean instability of the five mononucleotide repeats was 96.1% as compared with a mean instability of 69.8% for the three dinucleotide repeats of the NCI panel, indicating a superiority of mononucleotide repeats over dinucleotide repeats in detecting MSI. The fact that the two panels of markers detect the same set of MSI tumors is due to the presence of two mononucleotide repeats within the NCI panel. As demonstrated previously in gastric and colon MSI cases, the pentaplex PCR reaction using mononucleotide repeats is thus an easier and more sensitive method than the NCI panel, for the screening of MSI status in endometrial tumors.

Biomarkers, Tumor↗

Sensitivity of HCV RNA and HIV RNA blood screening assays.

BACKGROUND: The FDA requirement for sensitivity of viral NAT methods used in blood screening is a 95-percent detection limit of 100 copies per mL, whereas the NAT screening system should have a sensitivity of at least 5000 copies per mL per individual donation. According to the Common Technical Specifications of the European Directive 98/79/EC for in vitro diagnostics, viral standard dilutions (calibrated against the WHO standard) should be tested at least 24 times for a statistically valid assessment of the 95-percent detection limit. STUDY DESIGN AND METHODS: Viral standard dilution panels (PeliCheck, VQC-CLB) were prepared for HCV RNA genotypes 1 and 3 and for HIV RNA genotypes B and E. In a multicenter study, 23 laboratories tested the panels all together in 8 to 91 test runs per NAT method. RESULTS: The following 95-percent detection limits (and 95% CIs) were found on the HCV RNA genotype 1 reference panels (shown as geq/mL): Gen-Probe TMA, 85 (64-118); AmpliScreen, 126 (83-225); AmpliScreen with NucliSens Extractor, 21 (13-44); Amplicor with NucliSens Extractor, 69 (50-102), and Amplicor with Qiagen extraction technology, 144 (74-102). On HIV RNA genotype B dilution panels, the following 95-percent detection limits were found (shown as geq/mL): Gen-Probe TMA, 31 (20-52); AmpliScreen, 126 (67-311); AmpliScreen with NucliSens Extractor, 37 (23-69), and NucliSens QL assay, 123 (51-566). HIV RNA genotype E panels were detected with equal sensitivity as HIV RNA genotype B panels. In the Gen-Probe TMA assay, the 50-percent detection limits on HIV RNA type B and type E were 3.6 (2.6-5.0) and 3.9 (2.4-5.8) geq per mL, respectively. The HCV RNA genotype 1 and 3 standards were detected with equal sensitivity. CONCLUSION: The differences in sensitivity between NAT assays can be explained by the input of isolated viral nucleic acid in the amplification reactions. The FDA requirements for sensitivity of NAT blood screening assays can be met by the Gen-probe TMA, as well as by the AmpliScreen assays, particularly when combined with the NucliSens Extractor.

Adsorption↗

Rapid chromosomal assignment of medaka mutants by bulked segregant analysis.

Genetic screens in medaka are leading to the identification of an increasing number of unique mutant phenotypes. However, so far only a few genes responsible for these phenotypes have been characterized. Furthermore, no protocols using a systematic positional cloning strategy have been developed to determine the implicated genes. The PCR-based bulked segregant analysis is a fast and reliable tool to accomplish the initial steps of the positional cloning of a mutation. Here we describe the selection of a panel of genetic markers that, evenly distributed over the 24 chromosomes of medaka, provide a full coverage of the compact medaka genome (800 Mb) when used in bulked segregant analysis. The reference panel, which consists of 48 EST-derived markers, is anchored to a collection of more than 2000 polymorphic markers, thus facilitating a rapid transition from chromosomal assignment to fine mapping of the mutants. More importantly, since most of the genetic screens have been performed in the inbred Cab strain (derived from the Southern population), the selection of markers included in this panel was intended to optimize the recognition of polymorphisms between Cab and the polymorphic inbred mapping strain Kaga. Here we present a reliable mapping panel, confirmed both by the assignment of the locus responsible for the medaka mutation eyeless/Rx3 to chromosome 12, and by the analysis of its resolution power using representative markers.

Animals↗

Simplified hepatitis C virus genotyping by heteroduplex mobility analysis.

Heteroduplex mobility analysis (HMA) was used to genotype hepatitis C viruses (HCV) with PCR fragments derived from the 5' untranslated region (5'-UTR) or the NS5b region. HCV 5'-UTR fragments were amplified from 296 serum samples by use of a combined reverse transcription-PCR assay, and the genotypes of isolates were determined by sequencing. HCV genotype distributions in Australia were 39% for genotype 1a, 15% for 1b, 3% for 1a/b, <1% for 2a/c, 5% for 2b, 34% for 3a, <1% for 3b, and 1% for 4, and 1% of patients were infected with more than one genotype. Pairwise HMA of subtypes 1a, 1b, 2a/c, 2b, 3a, 3b, 4a, and 6a demonstrated that five distinct heteroduplex patterns were formed between the eight subtypes. A reference panel that contained a representative of each pattern (1a, 2b, 3a, 4a, and 6a) was used for genotyping. The pattern of heteroduplexes formed when a test isolate was mixed with the five reference isolates was correlated with the genotype, as determined by sequencing. Genotypes determined by HMA correlated exactly with sequencing results within the groups 1, 2, 3a, 3b/4, and 6. HMA was also used to simplify the identification of mixed infection with two HCV genotypes. In further studies, with amplicons from the NS5b region, HMA classified isolates into their respective subtypes, and the heteroduplex mobility ratio correlated closely with nucleotide sequence variation at the isolate, subtype, and genotype levels. HMA provides an adaptable, inexpensive, and rapid method of genotyping HCV that requires fewer resources than DNA sequencing.

5' Untranslated Regions↗

[Report of a new radioimmunologic technic for the assay of HBs antigen].

We tested a new radiometric assay (Hépatube Wellcome) using a complete automatic device, in hepatitis B surface antigen detection with I 125 marked antibody. The additional advantage of this reagent is its very long life-span (twelve weeks after the date of manufacture). The hepatube system is fully automatic, micro processor-controlled and designed to complete all washing and tracer addition steps in the hepatube test sequence after addition of the patient's sample. The results were compared in the same protocol with those obtained by the method currently used in our group (Ausria II 125). This study has been carried out on 7.589 sera or plasma samples; blood donors 5.352; medical and chirurgical patients 1.292; sera panel 87; repeated tests 367; positives and negatives control sera 421; assays ran the first day 70 The 153 positive results (2.3%) were confirmed by another assay before neutralisation. The sensitivity of both techniques was compared using a reference panel containing samples showing varying degrees of positivity, and representative of both main subtypes. We repeated the assay on this panel 2 months after issue of materials and again 3 months later. This new system is more sensitive than Ausria II 125. Of 6 644 patients the false positive was found in 1,1% of the cases, this was superior to the results found with Ausria II 125 but there is no false negative with this new method. There was no difference when serum or plasma was used.

False Positive Reactions↗

Toward a framework linkage map of the canine genome.

Selective breeding to maintain specific physical and behavioral traits has made the modern dog one of the most physically diverse species on earth. One unfortunate consequence of the common breeding practices used to develop lines of dogs with the desired traits is amplification and propagation of genetic diseases within distinct breeds. To map disease loci we have constructed a first-generation framework map of the canine genome. We developed large numbers of highly polymorphic markers, constructed a panel of canine-rodent hybrid cell lines, and assigned those markers to chromosome groups using the hybrid cell lines. Finally, we determined the order and spacing of markers on individual canine chromosomes by linkage analysis using a reference panel of 17 outbred pedigrees. This article describes approaches and strategies to accomplish these goals.

Animals↗

RFLP analysis of the HLA-, ChLA-, and RhLA-DQ alpha chain gene regions: conservation of restriction sites during evolution.

Genomic DNA samples, derived from a panel of 60 chimpanzees and 45 rhesus monkeys, were digested with the restriction enzymes Taq I and Bgl II and hybridized with an HLA-DQ alpha chain cDNA probe. The results were compared with the data available on a human reference panel. Use of the restriction enzyme Taq I and the DQ alpha chain probe allows the detection of five HLA-DQA1 and two HLA-DQA2 gene-associated fragments within the human population. For the ChLA and RhLA systems, 3 and 7 different DQA1-associated restriction patterns were detected, respectively, while for the chimpanzee a nonpolymorphic DQA2 (DX alpha) gene-associated fragment was also observed. The equivalent of the HLA- and ChLA-DQA2 genes appears to be absent in the rhesus monkey. The ChLA-DQA1 and -DQA2 gene-associated RFLP patterns are identical in man and chimpanzee, whereas such restriction site conservation is not seen in the rhesus monkey. The conclusion drawn is that the genetic organization of the HLA-DQA and ChLA-DQA gene regions, and possibly some of their allelic variabilities, already existed before man and chimpanzee separated in evolution. Moreover, the particular duplication which led to the generation of the HLA- and ChLA-DQA2 genes must have happened before speciation of members belonging to the superfamily Hominoidea (man, chimpanzee, etc), but probably after the separation of superfamily Cercopitecoidea (rhesus monkeys, baboons, etc.) from Hominoidea.

Animals↗