18 results on '"Paknia O"'
Search Results
2. A disorder clinically resembling cystic fibrosis caused by biallelic variants in the AGR2 gene.
- Author
-
Bertoli-Avella A, Hotakainen R, Al Shehhi M, Urzi A, Pareira C, Marais A, Al Shidhani K, Aloraimi S, Morales-Torres G, Fisher S, Demuth L, Moteleb Selim LA, Al Menabawy N, Busehail M, AlShaikh M, Gilani N, Chalabi DN, Alharbi NS, Alfadhel M, Abdelrahman M, Venselaar H, Anjum N, Saeed A, Alghamdi MA, Aljaedi H, Arabi H, Karageorgou V, Khan S, Hajjari Z, Radefeldt M, Al-Ali R, Tripolszki K, Jamhawi A, Paknia O, Cozma C, Cheema H, Ameziane N, Al-Muhsen S, and Bauer P
- Subjects
- Cystic Fibrosis Transmembrane Conductance Regulator genetics, Exome, Humans, Mutation, Phenotype, Cystic Fibrosis diagnosis, Cystic Fibrosis genetics, Mucoproteins genetics, Oncogene Proteins genetics
- Abstract
Purpose: We sought to describe a disorder clinically mimicking cystic fibrosis (CF) and to elucidate its genetic cause., Methods: Exome/genome sequencing and human phenotype ontology data of nearly 40 000 patients from our Bio/Databank were analysed. RNA sequencing of samples from the nasal mucosa from patients, carriers and controls followed by transcriptome analysis was performed., Results: We identified 13 patients from 9 families with a CF-like phenotype consisting of recurrent lower respiratory infections (13/13), failure to thrive (13/13) and chronic diarrhoea (8/13), with high morbidity and mortality. All patients had biallelic variants in AGR2 , (1) two splice-site variants, (2) gene deletion and (3) three missense variants. We confirmed aberrant AGR2 transcripts caused by an intronic variant and complete absence of AGR2 transcripts caused by the large gene deletion, resulting in loss of function (LoF). Furthermore, transcriptome analysis identified significant downregulation of components of the mucociliary machinery (intraciliary transport, cilium organisation), as well as upregulation of immune processes., Conclusion: We describe a previously unrecognised autosomal recessive disorder caused by AGR2 variants. AGR2 -related disease should be considered as a differential diagnosis in patients presenting a CF-like phenotype. This has implications for the molecular diagnosis and management of these patients. AGR2 LoF is likely the disease mechanism, with consequent impairment of the mucociliary defence machinery. Future studies should aim to establish a better understanding of the disease pathophysiology and to identify potential drug targets., Competing Interests: Competing interests: AB-A, RH, AU, CP, AM, GM-T, SF, LD, VK, SK, ZH, MR, RA-A, KT, AJ, OP, CC, NA and PB are employees of CENTOGENE GmbH. None of the other authors declared a potential conflict of interest., (© Author(s) (or their employer(s)) 2022. Re-use permitted under CC BY-NC. No commercial re-use. See rights and permissions. Published by BMJ.)
- Published
- 2022
- Full Text
- View/download PDF
3. An integrated multiomic approach as an excellent tool for the diagnosis of metabolic diseases: our first 3720 patients.
- Author
-
Almeida LS, Pereira C, Aanicai R, Schröder S, Bochinski T, Kaune A, Urzi A, Spohr TCLS, Viceconte N, Oppermann S, Alasel M, Ebadat S, Iftikhar S, Jasinge E, Elsayed SM, Tomoum H, Marzouk I, Jalan AB, Cerkauskaite A, Cerkauskiene R, Tkemaladze T, Nadeem AM, El Din Mahmoud IG, Mossad FA, Kamel M, Selim LA, Cheema HA, Paknia O, Cozma C, Juaristi-Manrique C, Guatibonza-Moreno P, Böttcher T, Vogel F, Pinto-Basto J, Bertoli-Avella A, and Bauer P
- Subjects
- Exome, High-Throughput Nucleotide Sequencing, Humans, Pakistan, Exome Sequencing, DNA Copy Number Variations, Metabolic Diseases diagnosis, Metabolic Diseases genetics
- Abstract
To present our experience using a multiomic approach, which integrates genetic and biochemical testing as a first-line diagnostic tool for patients with inherited metabolic disorders (IMDs). A cohort of 3720 patients from 62 countries was tested using a panel including 206 genes with single nucleotide and copy number variant (SNV/CNV) detection, followed by semi-automatic variant filtering and reflex biochemical testing (25 assays). In 1389 patients (37%), a genetic diagnosis was achieved. Within this cohort, the highest diagnostic yield was obtained for patients from Asia (57.5%, mainly from Pakistan). Overall, 701 pathogenic/likely pathogenic unique SNVs and 40 CNVs were identified. In 620 patients, the result of the biochemical tests guided variant classification and reporting. Top five diagnosed diseases were: Gaucher disease, Niemann-Pick disease type A/B, phenylketonuria, mucopolysaccharidosis type I, and Wilson disease. We show that integrated genetic and biochemical testing facilitated the decision on clinical relevance of the variants and led to a high diagnostic yield (37%), which is comparable to exome/genome sequencing. More importantly, up to 43% of these patients (n = 610) could benefit from medical treatments (e.g., enzyme replacement therapy). This multiomic approach constitutes a unique and highly effective tool for the genetic diagnosis of IMDs., (© 2022. The Author(s).)
- Published
- 2022
- Full Text
- View/download PDF
4. LRRK2 Loss-of-Function Variants in Patients with Rare Diseases: No Evidence for a Phenotypic Impact.
- Author
-
Beetz C, Westenberger A, Al-Ali R, Ameziane N, Alhashmi N, Boustany RM, Al Mutairi F, Alfadhel M, Al-Hassnan Z, AlSayed M, Kandaswamy KK, Paknia O, Skrahina V, Rolfs A, and Bauer P
- Subjects
- Humans, Leucine-Rich Repeat Serine-Threonine Protein Kinase-2 genetics, Protein Serine-Threonine Kinases, Rare Diseases
- Published
- 2021
- Full Text
- View/download PDF
5. Successful application of genome sequencing in a diagnostic setting: 1007 index cases from a clinically heterogeneous cohort.
- Author
-
Bertoli-Avella AM, Beetz C, Ameziane N, Rocha ME, Guatibonza P, Pereira C, Calvo M, Herrera-Ordonez N, Segura-Castel M, Diego-Alvarez D, Zawada M, Kandaswamy KK, Werber M, Paknia O, Zielske S, Ugrinovski D, Warnack G, Kampe K, Iurașcu MI, Cozma C, Vogel F, Alhashem A, Hertecant J, Al-Shamsi AM, Alswaid AF, Eyaid W, Al Mutairi F, Alfares A, Albalwi MA, Alfadhel M, Al-Sannaa NA, Reardon W, Alanay Y, Rolfs A, and Bauer P
- Subjects
- Adolescent, Child, Child, Preschool, Female, Gene Frequency, Genetic Diseases, Inborn epidemiology, Genetic Diseases, Inborn genetics, Genetic Testing statistics & numerical data, Humans, Infant, Infant, Newborn, Male, Prenatal Diagnosis standards, Prenatal Diagnosis statistics & numerical data, Sensitivity and Specificity, Exome Sequencing statistics & numerical data, Genetic Diseases, Inborn diagnosis, Genetic Testing standards, Exome Sequencing standards
- Abstract
Despite clear technical superiority of genome sequencing (GS) over other diagnostic methods such as exome sequencing (ES), few studies are available regarding the advantages of its clinical application. We analyzed 1007 consecutive index cases for whom GS was performed in a diagnostic setting over a 2-year period. We reported pathogenic and likely pathogenic (P/LP) variants that explain the patients' phenotype in 212 of the 1007 cases (21.1%). In 245 additional cases (24.3%), a variant of unknown significance (VUS) related to the phenotype was reported. We especially investigated patients which had had ES with no genetic diagnosis (n = 358). For this group, GS diagnostic yield was 14.5% (52 patients with P/LP out of 358). GS should be especially indicated for ES-negative cases since up to 29.6% of them could benefit from GS testing (14.5% with P/LP, n = 52 and 15.1% with VUS, n = 54). Genetic diagnoses in most of the ES-negative/GS-positive cases were determined by technical superiority of GS, i.e., access to noncoding regions and more uniform coverage. Importantly, we reported 79 noncoding variants, of which, 41 variants were classified as P/LP. Interpretation of noncoding variants remains challenging, and in many cases, complementary methods based on direct enzyme assessment, biomarker testing and RNA analysis are needed for variant classification and diagnosis. We present the largest cohort of patients with GS performed in a clinical setting to date. The results of this study should direct the decision for GS as standard second-line, or even first-line stand-alone test.
- Published
- 2021
- Full Text
- View/download PDF
6. Biallelic Pathogenic GFRA1 Variants Cause Autosomal Recessive Bilateral Renal Agenesis.
- Author
-
Arora V, Khan S, El-Hattab AW, Dua Puri R, Rocha ME, Merdzanic R, Paknia O, Beetz C, Rolfs A, Bertoli-Avella AM, Bauer P, and Verma IC
- Subjects
- Exome, Female, Genetic Counseling, Genetic Predisposition to Disease, Genetic Variation, Genome, Human, Homozygote, Humans, Kidney pathology, Kidney Diseases genetics, Male, Mutation, Pedigree, Sequence Analysis, DNA, Urinary Tract pathology, Alleles, Congenital Abnormalities genetics, Genes, Recessive, Glial Cell Line-Derived Neurotrophic Factor Receptors genetics, Kidney abnormalities, Kidney Diseases congenital
- Abstract
Background: Congenital anomalies of the kidney and urinary tract (CAKUT) are one of the most common malformations identified in the fetal stage. Bilateral renal agenesis (BRA) represents the most severe and fatal form of CAKUT. Only three genes have been confirmed to have a causal role in humans ( ITGA8 , GREB1L , and FGF20 )., Methods: Genome sequencing within a diagnostic setting and combined data repository analysis identified a novel gene., Results: Two patients presented with BRA, detected during the prenatal period, without additional recognizable malformations. They had parental consanguinity and similarly affected, deceased siblings, suggesting autosomal recessive inheritance. Evaluation of homozygous regions in patient 1 identified a novel, nonsense variant in GFRA1 (NM_001348097.1:c.676C>T, p.[Arg226*]). We identified 184 patients in our repository with renal agenesis and analyzed their exome/genome data. Of these 184 samples, 36 were from patients who presented with isolated renal agenesis. Two of them had loss-of-function variants in GFRA1 . The second patient was homozygous for a frameshift variant (NM_001348097.1:c.1294delA, p.[Thr432Profs*13]). The GFRA1 gene encodes a receptor on the Wolffian duct that regulates ureteric bud outgrowth in the development of a functional renal system, and has a putative role in the pathogenesis of Hirschsprung disease., Conclusions: These findings strongly support the causal role of GFRA1 -inactivating variants for an autosomal recessive, nonsyndromic form of BRA. This knowledge will enable early genetic diagnosis and better genetic counseling for families with BRA., (Copyright © 2021 by the American Society of Nephrology.)
- Published
- 2021
- Full Text
- View/download PDF
7. Genomic testing in 1019 individuals from 349 Pakistani families results in high diagnostic yield and clinical utility.
- Author
-
Cheema H, Bertoli-Avella AM, Skrahina V, Anjum MN, Waheed N, Saeed A, Beetz C, Perez-Lopez J, Rocha ME, Alawbathani S, Pereira C, Hovakimyan M, Patric IRP, Paknia O, Ameziane N, Cozma C, Bauer P, and Rolfs A
- Abstract
We implemented a collaborative diagnostic program in Lahore (Pakistan) aiming to establish the genetic diagnosis, and to asses diagnostic yield and clinical impact in patients with suspected genetic diseases. Local physicians ascertained pediatric patients who had no previous access to genetic testing. More than 1586 genetic tests were performed in 1019 individuals (349 index cases, 670 relatives). Most frequently performed tests were exome/genome sequencing (ES/GS, 284/78 index cases) and specific gene panels (55 index cases). In 61.3% of the patients ( n = 214) a genetic diagnosis was established based on pathogenic and likely pathogenic variants. Diagnostic yield was higher in consanguineous families (60.1 vs. 39.5%). In 27 patients, genetic diagnosis relied on additional biochemical testing, allowing rapid assessment of the functional effect of the variants. Remarkably, the genetic diagnosis had a direct impact on clinical management. Most relevant consequences were therapy related such as initiation of the appropriated treatment in a timely manner in 51.9% of the patients ( n = 111). Finally, we report 12 candidate genes among 66 cases with no genetic diagnosis. Importantly, three of these genes were validated as 'diagnostic' genes given the strong evidence supporting causality derived from our data repository (CAP2- dilated cardiomyopathy , ITFG2- intellectual disability and USP53- liver cholestasis). The high diagnostic yield, clinical impact, and research findings demonstrate the utility of genomic testing, especially when used as first-line genetic test. For patients with suspected genetic diseases from resource-limited regions, ES can be considered as the test of choice to achieve genetic diagnosis., Competing Interests: Competing interestsThe authors A.M.B.-A., V.S., C.B., J.P.-L., M.E.R., S.A., C.P., M.H., N.A., I.P., O.P., C.C., P.B., A.R. are employees at CENTOGENE, AG. None of the other authors declared a potential competing interest., (© The Author(s) 2020.)
- Published
- 2020
- Full Text
- View/download PDF
8. Repeated evolution of queen parthenogenesis and social hybridogenesis in Cataglyphis desert ants.
- Author
-
Kuhn A, Darras H, Paknia O, and Aron S
- Subjects
- Animals, Female, Genotype, Male, Phylogeny, Reproduction genetics, Social Behavior, Ants genetics, Arthropods genetics, Behavior, Animal physiology, Hybridization, Genetic genetics, Parthenogenesis genetics
- Abstract
Over the last decade, genetic studies on social insects have revealed a remarkable diversity of unusual reproductive strategies, such as male clonality, female clonality, and social hybridogenesis. In this context, Cataglyphis desert ants are useful models because of their unique reproductive systems. In several species, queens conditionally use sexual reproduction and parthenogenesis to produce sterile workers and reproductive queens, respectively. In social hybridogenesis, two distinct genetic lineages coexist within a population, and workers result from mating between partners of different lineages; in contrast, queens and males are both produced asexually by parthenogenesis. Consequently, nonreproductive workers are all interlineage hybrids, whereas reproductives are all pure lineage individuals. Here, we characterized the reproductive systems of 11 species to investigate the distribution of the conditional use of sex and social hybridogenesis in Cataglyphis. We identified one new case in which sexual reproduction was conditionally used in the absence of dependent-lineage reproduction. We also discovered five new instances of social hybridogenesis. Based on our phylogenetic analyses, we inferred that both the conditional use of sex and social hybridogenesis independently evolved multiple times in the genus Cataglyphis., (© 2019 John Wiley & Sons Ltd.)
- Published
- 2020
- Full Text
- View/download PDF
9. Development of an evidence-based algorithm that optimizes sensitivity and specificity in ES-based diagnostics of a clinically heterogeneous patient population.
- Author
-
Bauer P, Kandaswamy KK, Weiss MER, Paknia O, Werber M, Bertoli-Avella AM, Yüksel Z, Bochinska M, Oprea GE, Kishore S, Weckesser V, Karges E, and Rolfs A
- Subjects
- Genetic Diseases, Inborn diagnosis, Genetic Diseases, Inborn pathology, Genetic Variation genetics, High-Throughput Nucleotide Sequencing, Humans, Sequence Analysis, DNA, Exome genetics, Genetic Diseases, Inborn genetics, Exome Sequencing
- Abstract
Purpose: Next-generation sequencing (NGS) is rapidly replacing Sanger sequencing in genetic diagnostics. Sensitivity and specificity of NGS approaches are not well-defined, but can be estimated from applying NGS and Sanger sequencing in parallel. Utilizing this strategy, we aimed at optimizing exome sequencing (ES)-based diagnostics of a clinically diverse patient population., Methods: Consecutive DNA samples from unrelated patients with suspected genetic disease were exome-sequenced; comparatively nonstringent criteria were applied in variant calling. One thousand forty-eight variants in genes compatible with the clinical diagnosis were followed up by Sanger sequencing. Based on a set of variant-specific features, predictors for true positives and true negatives were developed., Results: Sanger sequencing confirmed 81.9% of ES-derived variants. Calls from the lower end of stringency accounted for the majority of the false positives, but also contained ~5% of the true positives. A predictor incorporating three variant-specific features classified 91.7% of variants with 100% specificity and 99.75% sensitivity. Confirmation status of the remaining variants (8.3%) was not predictable., Conclusions: Criteria for variant calling in ES-based diagnostics impact on specificity and sensitivity. Confirmatory sequencing for a proportion of variants, therefore, remains a necessity. Our study exemplifies how these variants can be defined on an empirical basis.
- Published
- 2019
- Full Text
- View/download PDF
10. Dominance-diversity relationships in ant communities differ with invasion.
- Author
-
Arnan X, Andersen AN, Gibb H, Parr CL, Sanders NJ, Dunn RR, Angulo E, Baccaro FB, Bishop TR, Boulay R, Castracani C, Cerdá X, Toro ID, Delsinne T, Donoso DA, Elten EK, Fayle TM, Fitzpatrick MC, Gómez C, Grasso DA, Grossman BF, Guénard B, Gunawardene N, Heterick B, Hoffmann BD, Janda M, Jenkins CN, Klimes P, Lach L, Laeger T, Leponce M, Lucky A, Majer J, Menke S, Mezger D, Mori A, Moses J, Munyai TC, Paknia O, Pfeiffer M, Philpott SM, Souza JLP, Tista M, Vasconcelos HL, and Retana J
- Subjects
- Animals, Climate, Ecosystem, Ants physiology, Biodiversity
- Abstract
The relationship between levels of dominance and species richness is highly contentious, especially in ant communities. The dominance-impoverishment rule states that high levels of dominance only occur in species-poor communities, but there appear to be many cases of high levels of dominance in highly diverse communities. The extent to which dominant species limit local richness through competitive exclusion remains unclear, but such exclusion appears more apparent for non-native rather than native dominant species. Here we perform the first global analysis of the relationship between behavioral dominance and species richness. We used data from 1,293 local assemblages of ground-dwelling ants distributed across five continents to document the generality of the dominance-impoverishment rule, and to identify the biotic and abiotic conditions under which it does and does not apply. We found that the behavioral dominance-diversity relationship varies greatly, and depends on whether dominant species are native or non-native, whether dominance is considered as occurrence or relative abundance, and on variation in mean annual temperature. There were declines in diversity with increasing dominance in invaded communities, but diversity increased with increasing dominance in native communities. These patterns occur along the global temperature gradient. However, positive and negative relationships are strongest in the hottest sites. We also found that climate regulates the degree of behavioral dominance, but differently from how it shapes species richness. Our findings imply that, despite strong competitive interactions among ants, competitive exclusion is not a major driver of local richness in native ant communities. Although the dominance-impoverishment rule applies to invaded communities, we propose an alternative dominance-diversification rule for native communities., (© 2018 John Wiley & Sons Ltd.)
- Published
- 2018
- Full Text
- View/download PDF
11. Biallelic inactivating variants in the GTPBP2 gene cause a neurodevelopmental disorder with severe intellectual disability.
- Author
-
Bertoli-Avella AM, Garcia-Aznar JM, Brandau O, Al-Hakami F, Yüksel Z, Marais A, Grüning NM, Abbasi Moheb L, Paknia O, Alshaikh N, Alameer S, Marafi MJ, Al-Mulla F, Al-Sannaa N, Rolfs A, and Bauer P
- Subjects
- Agenesis of Corpus Callosum pathology, Alleles, Child, Female, GTP-Binding Proteins, Humans, Intellectual Disability pathology, Iron Overload pathology, Male, Phenotype, Syndrome, Agenesis of Corpus Callosum genetics, Intellectual Disability genetics, Iron Overload genetics, Loss of Function Mutation, Monomeric GTP-Binding Proteins genetics
- Abstract
Congenital neurological disorders are genetically highly heterogeneous. Rare forms of hereditary neurological disorders are still difficult to be adequately diagnosed. Pertinent studies, especially when reporting only single families, need independent confirmation. We present three unrelated families in which whole-exome sequencing identified the homozygous non-sense variants c.430[C>T];[C>T] p.(Arg144*), c.1219[C>T];[C>T] p.(Gln407*) and c.1408[C>T];[C>T] p.(Arg470*) in GTPBP2. Their clinical presentations include early onset and apparently non-progressive motor and cognitive impairment, and thereby overlap with findings in a recently described family harbouring a homozygous GTPBP2 splice site variant. Notable differences include structural brain abnormalities (e.g., agenesis of the corpus callosum, exclusive to our patients), and evidence for brain iron accumulation (exclusive to the previously described family). This report confirms pathogenicity of biallelic GTPBP2 inactivation and broadens the phenotypic spectrum. It also underlines that a potential involvement of brain iron accumulation needs clarification. Further patients will have to be identified and characterised in order to fully define the core features of GTPBP2-associated neurological disorder, but future approaches to molecular diagnosis of neurodevelopmental disorders should implement GTPBP2.
- Published
- 2018
- Full Text
- View/download PDF
12. The marker choice: Unexpected resolving power of an unexplored CO1 region for layered DNA barcoding approaches.
- Author
-
Rach J, Bergmann T, Paknia O, DeSalle R, Schierwater B, and Hadrys H
- Subjects
- Animals, Genetic Markers, Odonata classification, DNA Barcoding, Taxonomic, DNA, Mitochondrial genetics, Insect Proteins genetics, Mitochondrial Proteins genetics, NADH Dehydrogenase genetics, Odonata genetics
- Abstract
The potential of DNA barcoding approaches to identify single species and characterize species compositions strongly depends on the marker choice. The prominent "Folmer region", a 648 basepair fragment at the 5' end of the mitochondrial CO1 gene, has been traditionally applied as a universal DNA barcoding region for metazoans. In order to find a suitable marker for biomonitoring odonates (dragonflies and damselflies), we here explore a new region of the CO1 gene (CO1B) for DNA barcoding in 51 populations of 23 dragonfly and damselfly species. We compare the "Folmer region", the mitochondrial ND1 gene (NADH dehydrogenase 1) and the new CO1 region with regard to (i) speed and reproducibility of sequence generation, (ii) levels of homoplasy and (iii) numbers of diagnostic characters for discriminating closely related sister taxa and populations. The performances of the gene regions regarding these criteria were quite different. Both, the amplification of CO1B and ND1 was highly reproducible and CO1B showed the highest potential for discriminating sister taxa at different taxonomic levels. In contrast, the amplification of the "Folmer region" using the universal primers was difficult and the third codon positions of this fragment have experienced nucleotide substitution saturation. Most important, exploring this new barcode region of the CO1 gene identified a higher discriminating power between closely related sister taxa. Together with the design of layered barcode approaches adapted to the specific taxonomic "environment", this new marker will further enhance the discrimination power at the species level.
- Published
- 2017
- Full Text
- View/download PDF
13. A global database of ant species abundances.
- Author
-
Gibb H, Dunn RR, Sanders NJ, Grossman BF, Photakis M, Abril S, Agosti D, Andersen AN, Angulo E, Armbrecht I, Arnan X, Baccaro FB, Bishop TR, Boulay R, Brühl C, Castracani C, Cerda X, Del Toro I, Delsinne T, Diaz M, Donoso DA, Ellison AM, Enriquez ML, Fayle TM, Feener DH Jr, Fisher BL, Fisher RN, Fitzpatrick MC, Gómez C, Gotelli NJ, Gove A, Grasso DA, Groc S, Guenard B, Gunawardene N, Heterick B, Hoffmann B, Janda M, Jenkins C, Kaspari M, Klimes P, Lach L, Laeger T, Lattke J, Leponce M, Lessard JP, Longino J, Lucky A, Luke SH, Majer J, McGlynn TP, Menke S, Mezger D, Mori A, Moses J, Munyai TC, Pacheco R, Paknia O, Pearce-Duvet J, Pfeiffer M, Philpott SM, Resasco J, Retana J, Silva RR, Sorger MD, Souza J, Suarez A, Tista M, Vasconcelos HL, Vonshak M, Weiser MD, Yates M, and Parr CL
- Subjects
- Animals, Ants classification, Ecosystem, Ants physiology, Databases, Factual, Ecology
- Abstract
What forces structure ecological assemblages? A key limitation to general insights about assemblage structure is the availability of data that are collected at a small spatial grain (local assemblages) and a large spatial extent (global coverage). Here, we present published and unpublished data from 51 ,388 ant abundance and occurrence records of more than 2,693 species and 7,953 morphospecies from local assemblages collected at 4,212 locations around the world. Ants were selected because they are diverse and abundant globally, comprise a large fraction of animal biomass in most terrestrial communities, and are key contributors to a range of ecosystem functions. Data were collected between 1949 and 2014, and include, for each geo-referenced sampling site, both the identity of the ants collected and details of sampling design, habitat type, and degree of disturbance. The aim of compiling this data set was to provide comprehensive species abundance data in order to test relationships between assemblage structure and environmental and biogeographic factors. Data were collected using a variety of standardized methods, such as pitfall and Winkler traps, and will be valuable for studies investigating large-scale forces structuring local assemblages. Understanding such relationships is particularly critical under current rates of global change. We encourage authors holding additional data on systematically collected ant assemblages, especially those in dry and cold, and remote areas, to contact us and contribute their data to this growing data set., (© 2016 by the Ecological Society of America.)
- Published
- 2017
- Full Text
- View/download PDF
14. Clinical exome sequencing: results from 2819 samples reflecting 1000 families.
- Author
-
Trujillano D, Bertoli-Avella AM, Kumar Kandaswamy K, Weiss ME, Köster J, Marais A, Paknia O, Schröder R, Garcia-Aznar JM, Werber M, Brandau O, Calvo Del Castillo M, Baldi C, Wessel K, Kishore S, Nahavandi N, Eyaid W, Al Rifai MT, Al-Rumayyan A, Al-Twaijri W, Alothaim A, Alhashem A, Al-Sannaa N, Al-Balwi M, Alfadhel M, Rolfs A, and Abou Jamra R
- Subjects
- Adolescent, Adult, Child, Child, Preschool, Female, Flavoproteins genetics, Genetic Testing standards, Genotyping Techniques standards, Humans, Infant, Infant, Newborn, Intracellular Signaling Peptides and Proteins genetics, Male, Middle Aged, Mitochondrial Proteins genetics, NAV1.3 Voltage-Gated Sodium Channel genetics, Nuclear Family, Phenotype, Potassium Channels genetics, Protein Tyrosine Phosphatases, Non-Receptor genetics, Protoporphyrinogen Oxidase genetics, Sequence Analysis, DNA standards, Sodium Channels genetics, Voltage-Gated Sodium Channel beta-1 Subunit genetics, Exome, Genetic Testing methods, Genotyping Techniques methods, Sequence Analysis, DNA methods
- Abstract
We report our results of 1000 diagnostic WES cases based on 2819 sequenced samples from 54 countries with a wide phenotypic spectrum. Clinical information given by the requesting physicians was translated to HPO terms. WES processes were performed according to standardized settings. We identified the underlying pathogenic or likely pathogenic variants in 307 families (30.7%). In further 253 families (25.3%) a variant of unknown significance, possibly explaining the clinical symptoms of the index patient was identified. WES enabled timely diagnosing of genetic diseases, validation of causality of specific genetic disorders of PTPN23, KCTD3, SCN3A, PPOX, FRMPD4, and SCN1B, and setting dual diagnoses by detecting two causative variants in distinct genes in the same patient. We observed a better diagnostic yield in consanguineous families, in severe and in syndromic phenotypes. Our results suggest that WES has a better yield in patients that present with several symptoms, rather than an isolated abnormality. We also validate the clinical benefit of WES as an effective diagnostic tool, particularly in nonspecific or heterogeneous phenotypes. We recommend WES as a first-line diagnostic in all cases without a clear differential diagnosis, to facilitate personal medical care., Competing Interests: DT, AMBA, MERW, JK, KKK, AM, OP, MCdC, CB, KW, RS, JMGA, OB, SK, NN, MW, RAJ are employed at Centogene AG; AR has financial holdings in Centogene AG; WE, MTAR, AAR, WAT, AAlo, MAB, and MA are employees at King Abdulaziz Medical city; AAlh is employee at Prince Sultan Military Medical City; NAS is employee at Johns Hopkins Aramco hospital.
- Published
- 2017
- Full Text
- View/download PDF
15. The most primitive metazoan animals, the placozoans, show high sensitivity to increasing ocean temperatures and acidities.
- Author
-
Schleicherová D, Dulias K, Osigus HJ, Paknia O, Hadrys H, and Schierwater B
- Abstract
The increase in atmospheric carbon dioxide (CO
2 ) leads to rising temperatures and acidification in the oceans, which directly or indirectly affects all marine organisms, from bacteria to animals. We here ask whether the simplest-and possibly also the oldest-metazoan animals, the placozoans, are particularly sensitive to ocean warming and acidification. Placozoans are found in all warm and temperate oceans and are soft-bodied, microscopic invertebrates lacking any calcified structures, organs, or symmetry. We here show that placozoans respond highly sensitive to temperature and acidity stress. The data reveal differential responses in different placozoan lineages and encourage efforts to develop placozoans as a potential biomarker system.- Published
- 2017
- Full Text
- View/download PDF
16. Global Habitat Suitability and Ecological Niche Separation in the Phylum Placozoa.
- Author
-
Paknia O and Schierwater B
- Subjects
- Animal Distribution physiology, Animals, Bayes Theorem, Caribbean Region, Ecosystem, Mediterranean Sea, Pacific Ocean, Phylogeography, Placozoa classification, Temperature, Genetic Speciation, Phylogeny, Placozoa genetics, RNA, Ribosomal, 16S genetics
- Abstract
The enigmatic placozoans, which hold a key position in the metazoan Tree of Life, have attracted substantial attention in many areas of biological and biomedical research. While placozoans have become an emerging model system, their ecology and particularly biogeography remain widely unknown. In this study, we use modelling approaches to explore habitat preferences, and distribution pattern of the placozoans phylum. We provide hypotheses for discrete ecological niche separation between genetic placozoan lineages, which may also help to understand biogeography patterns in other small marine invertebrates. We, here, used maximum entropy modelling to predict placozoan distribution using 20 environmental grids of 9.2 km2 resolution. In addition, we used recently developed metrics of niche overlap to compare habitat suitability models of three genetic clades. The predicted distributions range from 55°N to 44°S and are restricted to regions of intermediate to warm sea surface temperatures. High concentrations of salinity and low nutrient concentrations appear as secondary factors. Tests of niche equivalency reveal the largest differences between placozoan clades I and III. Interestingly, the genetically well-separated clades I and V appear to be ecologically very similar. Our habitat suitability models predict a wider latitudinal distribution for placozoans, than currently described, especially in the northern hemisphere. With respect to biogeography modelling, placozoans show patterns somewhere between higher metazoan taxa and marine microorganisms, with the first group usually showing complex biogeographies and the second usually showing "no biogeography."
- Published
- 2015
- Full Text
- View/download PDF
17. Some 'ant'swers: Application of a layered barcode approach to problems in ant taxonomy.
- Author
-
Paknia O, Bergmann T, and Hadrys H
- Subjects
- Animals, Electron Transport Complex IV genetics, RNA, Ribosomal, 28S genetics, Rhodopsin genetics, Ants classification, Ants genetics, Computational Biology methods, DNA Barcoding, Taxonomic methods, Genetic Variation
- Abstract
DNA barcoding has emerged as a routine tool in modern taxonomy. Although straightforward, this approach faces new challenges, when applied to difficult situation such as defining cryptic biodiversity. Ants are prime examples for high degrees of cryptic biodiversity due to complex population differentiation, hybridization and speciation processes. Here, we test the DNA barcoding region, cytochrome c oxidase 1 and two supplementary markers, 28S ribosomal DNA and long-wavelength rhodopsin, commonly used in ant taxonomy, for their potential in a layered, character-based barcoding approach across different taxonomic levels. Furthermore, we assess performance of the character-based barcoding approach to determine cryptic species diversity in ants. We found (i) that the barcode potential of a specific genetic marker varied widely among taxonomic levels in ants; (ii) that application of a layered, character-based barcode for identification of specimens can be a solution to taxonomical challenging groups; (iii) that the character-based barcoding approach allows us to differentiate specimens even within locations based on pure characters. In summary, (layered) character-based barcoding offers a reliable alternative for problematic species identification in ants and can be used as a fast and cost-efficient approach to estimate presence, absence or frequency of cryptic species., (© 2015 John Wiley & Sons Ltd.)
- Published
- 2015
- Full Text
- View/download PDF
18. Climate mediates the effects of disturbance on ant assemblage structure.
- Author
-
Gibb H, Sanders NJ, Dunn RR, Watson S, Photakis M, Abril S, Andersen AN, Angulo E, Armbrecht I, Arnan X, Baccaro FB, Bishop TR, Boulay R, Castracani C, Del Toro I, Delsinne T, Diaz M, Donoso DA, Enríquez ML, Fayle TM, Feener DH Jr, Fitzpatrick MC, Gómez C, Grasso DA, Groc S, Heterick B, Hoffmann BD, Lach L, Lattke J, Leponce M, Lessard JP, Longino J, Lucky A, Majer J, Menke SB, Mezger D, Mori A, Munyai TC, Paknia O, Pearce-Duvet J, Pfeiffer M, Philpott SM, de Souza JL, Tista M, Vasconcelos HL, Vonshak M, and Parr CL
- Subjects
- Animals, Climate Change, Temperature, Ants physiology, Biodiversity, Climate
- Abstract
Many studies have focused on the impacts of climate change on biological assemblages, yet little is known about how climate interacts with other major anthropogenic influences on biodiversity, such as habitat disturbance. Using a unique global database of 1128 local ant assemblages, we examined whether climate mediates the effects of habitat disturbance on assemblage structure at a global scale. Species richness and evenness were associated positively with temperature, and negatively with disturbance. However, the interaction among temperature, precipitation and disturbance shaped species richness and evenness. The effect was manifested through a failure of species richness to increase substantially with temperature in transformed habitats at low precipitation. At low precipitation levels, evenness increased with temperature in undisturbed sites, peaked at medium temperatures in disturbed sites and remained low in transformed sites. In warmer climates with lower rainfall, the effects of increasing disturbance on species richness and evenness were akin to decreases in temperature of up to 9°C. Anthropogenic disturbance and ongoing climate change may interact in complicated ways to shape the structure of assemblages, with hot, arid environments likely to be at greatest risk., (© 2015 The Author(s) Published by the Royal Society. All rights reserved.)
- Published
- 2015
- Full Text
- View/download PDF
Catalog
Discovery Service for Jio Institute Digital Library
For full access to our library's resources, please sign in.