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1.
Phys Chem Chem Phys ; 26(20): 14970-14979, 2024 May 22.
Article in English | MEDLINE | ID: mdl-38739372

ABSTRACT

Curcumin is a medicinal agent that exhibits anti-cancer and anti-Alzheimer's disease properties. It has a keto-enol moiety that gives rise to many of its chemical properties including metal complexation and acid-base equilibria. A previous study has shown that keto-enol tautomerization at this moiety is implicated in the anti-Alzheimer's disease effect of curcumin, highlighting the importance of this process. In this study, tautomerization of curcumin in methanol, acetone and acetonitrile was investigated using time-resolved 1H nuclear magnetic resonance spectroscopy. Curcumin undergoes hydrogen-deuterium exchange with the solvents and the proton resonance peak corresponding to the hydrogen at the α-carbon position (Cα) decays as a function of time, signifying deuteration at this position. Because tautomerization is the rate limiting step in the deuteration of curcumin at the Cα position, the rate of tautomerization is inferred from the rate of deuteration. The rate constant of tautomerization of curcumin shows a temperature dependence and analysis using the Arrhenius equation revealed activation energies (Ea) of tautomerization of (80.1 ± 5.9), (64.1 ± 1.0) and (68.3 ± 5.5) kJ mol-1 in methanol, D2O/acetone and D2O/acetonitrile, respectively. Insight into the role of water in tautomerization of curcumin was further offered by density functional theory studies. The transition state of tautomerization was optimized in the presence of water molecules. The results show a hydrogen-bonded solvent bridge between the diketo moiety and Cα of curcumin. The Ea of tautomerization of curcumin shows a strong dependence on the number of water molecules in the solvent bridge, indicating the critical role played by the solvent bridge in catalyzing tautomerization of curcumin.


Subject(s)
Curcumin , Curcumin/chemistry , Methanol/chemistry , Acetonitriles/chemistry , Acetone/chemistry , Isomerism , Thermodynamics , Solvents/chemistry
2.
J Mol Diagn ; 25(7): 411-427, 2023 07.
Article in English | MEDLINE | ID: mdl-37207865

ABSTRACT

Clinical laboratory implementation of next-generation sequencing (NGS)-based constitutional genetic testing has been rapid and widespread. In the absence of widely adopted comprehensive guidance, there remains substantial variability among laboratories in the practice of NGS. One issue of sustained discussion in the field is whether and to what extent orthogonal confirmation of genetic variants identified by NGS is necessary or helpful. The Association for Molecular Pathology Clinical Practice Committee convened the NGS Germline Variant Confirmation Working Group to assess current evidence regarding orthogonal confirmation and to establish recommendations for standardizing orthogonal confirmation practices to support quality patient care. On the basis of the results of a survey of the literature, a survey of laboratory practices, and subject expert matter consensus, eight recommendations are presented, providing a common framework for clinical laboratory professionals to develop or refine individualized laboratory policies and procedures regarding orthogonal confirmation of germline variants detected by NGS.


Subject(s)
Counselors , Pathology, Molecular , Humans , Genetic Testing/methods , High-Throughput Nucleotide Sequencing/methods , Germ Cells
3.
Cancers (Basel) ; 14(10)2022 May 13.
Article in English | MEDLINE | ID: mdl-35626031

ABSTRACT

Consensus guidelines for hereditary breast and ovarian cancer include management recommendations for pathogenic/likely pathogenic (P/LP) variants in ATM, CHEK2, PALB2, and other DNA damage repair (DDR) genes beyond BRCA1 or BRCA2. We report on clinical management decisions across three academic medical centers resulting from P/LP findings in DDR genes in breast/ovarian cancer patients. Among 2184 patients, 156 (7.1%) carried a P/LP variant in a DDR gene. Clinical follow-up information was available for 101/156 (64.7%) patients. Genetic test result-based management recommendations were made for 57.8% (n = 59) of patients and for 64.7% (n = 66) of patients' family members. Most recommendations were made for moderate-to-high risk genes and were consistent with guidelines. Sixty-six percent of patients (n = 39/59) implemented recommendations. This study suggests that P/LP variants in DDR genes beyond BRCA1 and BRCA2 can change clinical management recommendations for patients and their family members, facilitate identification of new at-risk carriers, and impact treatment decisions. Additional efforts are needed to improve the implementation rates of genetic-testing-based management recommendations for patients and their family members.

4.
Nat Biotechnol ; 40(5): 672-680, 2022 05.
Article in English | MEDLINE | ID: mdl-35132260

ABSTRACT

The repetitive nature and complexity of some medically relevant genes poses a challenge for their accurate analysis in a clinical setting. The Genome in a Bottle Consortium has provided variant benchmark sets, but these exclude nearly 400 medically relevant genes due to their repetitiveness or polymorphic complexity. Here, we characterize 273 of these 395 challenging autosomal genes using a haplotype-resolved whole-genome assembly. This curated benchmark reports over 17,000 single-nucleotide variations, 3,600 insertions and deletions and 200 structural variations each for human genome reference GRCh37 and GRCh38 across HG002. We show that false duplications in either GRCh37 or GRCh38 result in reference-specific, missed variants for short- and long-read technologies in medically relevant genes, including CBS, CRYAA and KCNE1. When masking these false duplications, variant recall can improve from 8% to 100%. Forming benchmarks from a haplotype-resolved whole-genome assembly may become a prototype for future benchmarks covering the whole genome.


Subject(s)
Genome, Human , Genome, Human/genetics , Haplotypes/genetics , Humans , Sequence Analysis, DNA
5.
Genet Med ; 23(9): 1673-1680, 2021 09.
Article in English | MEDLINE | ID: mdl-34007000

ABSTRACT

PURPOSE: To evaluate the impact of technically challenging variants on the implementation, validation, and diagnostic yield of commonly used clinical genetic tests. Such variants include large indels, small copy-number variants (CNVs), complex alterations, and variants in low-complexity or segmentally duplicated regions. METHODS: An interlaboratory pilot study used synthetic specimens to assess detection of challenging variant types by various next-generation sequencing (NGS)-based workflows. One well-performing workflow was further validated and used in clinician-ordered testing of more than 450,000 patients. RESULTS: In the interlaboratory study, only 2 of 13 challenging variants were detected by all 10 workflows, and just 3 workflows detected all 13. Limitations were also observed among 11 less-challenging indels. In clinical testing, 21.6% of patients carried one or more pathogenic variants, of which 13.8% (17,561) were classified as technically challenging. These variants were of diverse types, affecting 556 of 1,217 genes across hereditary cancer, cardiovascular, neurological, pediatric, reproductive carrier screening, and other indicated tests. CONCLUSION: The analytic and clinical sensitivity of NGS workflows can vary considerably, particularly for prevalent, technically challenging variants. This can have important implications for the design and validation of tests (by laboratories) and the selection of tests (by clinicians) for a wide range of clinical indications.


Subject(s)
Genetic Testing , High-Throughput Nucleotide Sequencing , Child , DNA Copy Number Variations/genetics , Humans , INDEL Mutation/genetics , Pilot Projects
6.
JAMA Netw Open ; 3(10): e2019452, 2020 10 01.
Article in English | MEDLINE | ID: mdl-33026450

ABSTRACT

Importance: Both germline genetic testing and tumor DNA sequencing are increasingly used in cancer care. The indications for testing and utility of these 2 tests differ, and guidelines recommend that germline analysis follow tumor sequencing in certain patients to determine whether particular variants are of somatic or germline origin. Broad clinical experience with such follow-up testing has not yet been thoroughly described. Objective: To examine the yield and utility of germline testing following tumor DNA sequencing in a large, diverse patient population. Design, Setting, and Participants: A retrospective cohort study examined germline testing through a laboratory supporting multiple academic and community clinics. Participants included 2023 patients with cancer who received germline testing and previously underwent tumor DNA sequencing. These patients received germline testing between January 5, 2015, and January 31, 2020, although most (81% of patients) received testing between January 2, 2018, and January 31, 2020. Main Outcomes and Measures: The prevalence of pathogenic germline variants (PGVs) was calculated by gene, cancer type, and age at diagnosis. Potential actionability of these findings was determined based on current management guidelines, precision therapy labels, and clinical trial eligibility criteria. Patient records were reviewed to determine whether germline follow-up testing would have been recommended by current guidelines. Results: Among 2023 eligible patients, 1085 were female (53.6%), and the median age at cancer diagnosis was 56 (range, 0-92) years. Pathogenic germline variants were detected in 617 patients (30.5%; 95% CI, 28.5%-32.6%) and were prevalent across patient ages (1-85 years) and cancer types, including cancers known to be strongly associated with germline variance (eg, breast, colorectal) as well as others (eg, renal, lung, and bladder). Many patients (78%-82%) with PGVs met criteria for germline follow-up testing, and 8.1% of PGVs were missed by tumor sequencing. Among those with germline-positive findings, 69 patients (11.2%) had PGVs identified only after presenting with a second primary cancer that possibly could have been detected earlier or prevented given current gene-specific surveillance and risk-reduction recommendations. Conclusions and Relevance: The findings of this study suggest that germline analysis following tumor sequencing often produces findings that may impact patient care by influencing systemic therapy choices, surgical decisions, additional cancer screening, and genetic counseling in families. Current guidelines and tumor testing approaches appear to capture many, but not all, of these germline findings, reinforcing the utility of both expanded germline follow-up testing as well as germline analysis independent of tumor sequencing in appropriate patients.


Subject(s)
Early Detection of Cancer/statistics & numerical data , Gene Expression Profiling/methods , Genetic Testing/statistics & numerical data , Germ Cells/pathology , Neoplasms/diagnosis , Adolescent , Adult , Aged , Aged, 80 and over , Biomarkers, Tumor , Child , Child, Preschool , DNA Mutational Analysis , Female , Humans , Infant , Infant, Newborn , Male , Middle Aged , Neoplasms/pathology , Neoplasms/therapy , Prognosis , Retrospective Studies , Risk Assessment , Young Adult
7.
Mol Cell Proteomics ; 19(8): 1310-1329, 2020 08.
Article in English | MEDLINE | ID: mdl-32430394

ABSTRACT

The fungal cell-wall integrity signaling (CWIS) pathway regulates cellular response to environmental stress to enable wall repair and resumption of normal growth. This complex, interconnected, pathway has been only partially characterized in filamentous fungi. To better understand the dynamic cellular response to wall perturbation, a ß-glucan synthase inhibitor (micafungin) was added to a growing A. nidulans shake-flask culture. From this flask, transcriptomic and phosphoproteomic data were acquired over 10 and 120 min, respectively. To differentiate statistically-significant dynamic behavior from noise, a multivariate adaptive regression splines (MARS) model was applied to both data sets. Over 1800 genes were dynamically expressed and over 700 phosphorylation sites had changing phosphorylation levels upon micafungin exposure. Twelve kinases had altered phosphorylation and phenotypic profiling of all non-essential kinase deletion mutants revealed putative connections between PrkA, Hk-8-4, and Stk19 and the CWIS pathway. Our collective data implicate actin regulation, endocytosis, and septum formation as critical cellular processes responding to activation of the CWIS pathway, and connections between CWIS and calcium, HOG, and SIN signaling pathways.


Subject(s)
Aspergillus nidulans/genetics , Aspergillus nidulans/metabolism , Cell Wall/metabolism , Fungal Proteins/genetics , Phosphoproteins/genetics , Proteomics , Stress, Physiological/genetics , Transcriptome/genetics , Amino Acid Sequence , Aspergillus nidulans/drug effects , Aspergillus nidulans/growth & development , Cell Wall/drug effects , Fungal Proteins/chemistry , Fungal Proteins/metabolism , Gene Expression Regulation, Fungal/drug effects , Micafungin/pharmacology , Models, Biological , Mutation/genetics , Phosphoproteins/chemistry , Phosphoproteins/metabolism , Phosphorylation/drug effects , Protein Kinases/metabolism , RNA-Seq , Reproducibility of Results , Stress, Physiological/drug effects , Transcriptome/drug effects
8.
mBio ; 10(2)2019 04 30.
Article in English | MEDLINE | ID: mdl-31040248

ABSTRACT

In filamentous fungi, an important kinase responsible for adaptation to changes in available nutrients is cyclic AMP (cAMP)-dependent protein kinase (protein kinase A [PKA]). This kinase has been well characterized at a molecular level, but its systemic action and direct/indirect targets are generally not well understood in filamentous fungi. In this work, we used a pkaA deletion strain (ΔpkaA) to identify Aspergillus nidulans proteins for which phosphorylation is dependent (either directly or indirectly) on PKA. A combination of phosphoproteomic and transcriptomic analyses revealed both direct and indirect targets of PKA and provided a global perspective on its function. One of these targets was the transcription factor CreA, the main repressor responsible for carbon catabolite repression (CCR). In the ΔpkaA strain, we identified a previously unreported phosphosite in CreA, S319, which (based on motif analysis) appears to be a direct target of Stk22 kinase (AN5728). Upon replacement of CreA S319 with an alanine (i.e., phosphonull mutant), the dynamics of CreA import to the nucleus are affected. Collectively, this work provides a global overview of PKA function while also providing novel insight regarding significance of a specific PKA-mediated phosphorylation event.IMPORTANCE The cyclic AMP (cAMP)-dependent protein kinase A (PKA) signaling pathway is well conserved across eukaryotes, and previous work has shown that it plays an important role in regulating development, growth, and virulence in a number of fungi. PKA is activated in response to extracellular nutrients and acts to regulate metabolism and growth. While a number of components in the PKA pathway have been defined in filamentous fungi, current understanding does not provide a global perspective on PKA function. Thus, this work is significant in that it comprehensively identifies proteins and functional pathways regulated by PKA in a model filamentous fungus. This information enhances our understanding of PKA action and may provide information on how to manipulate it for specific purposes.


Subject(s)
Aspergillus nidulans/genetics , Aspergillus nidulans/metabolism , Cyclic AMP-Dependent Protein Kinases/metabolism , Fungal Proteins/metabolism , Gene Expression Regulation, Bacterial , Phosphoproteins/analysis , Protein Processing, Post-Translational , Repressor Proteins/metabolism , Aspergillus nidulans/chemistry , Fungal Proteins/genetics , Gene Deletion , Gene Expression Profiling , Proteome/analysis , Repressor Proteins/genetics
9.
Fungal Genet Biol ; 125: 1-12, 2019 04.
Article in English | MEDLINE | ID: mdl-30639305

ABSTRACT

The protein kinase MpkA plays a prominent role in the cell wall integrity signaling (CWIS) pathway, acting as the terminal MAPK activating expression of genes which encode cell wall biosynthetic enzymes and other repair functions. Numerous studies focus on MpkA function during cell wall perturbation. Here, we focus on the role MpkA plays outside of cell wall stress, during steady state growth. In an effort to seek other, as yet unknown, connections to this pathway, an mpkA deletion mutant (ΔmpkA) was subjected to phosphoproteomic and transcriptomic analysis. When compared to the control (isogenic parent of ΔmpkA), there is strong evidence suggesting MpkA is involved with maintaining cell wall strength, branching regulation, and the iron starvation pathway, among others. Particle-size analysis during shake flask growth revealed ΔmpkA mycelia were about 4 times smaller than the control strain and more than 90 cell wall related genes show significantly altered expression levels. The deletion mutant had a significantly higher branching rate than the control and phosphoproteomic results show putative branching-regulation proteins, such as CotA, LagA, and Cdc24, have a significantly different level of phosphorylation. When grown in iron limited conditions, ΔmpkA had no difference in growth rate or production of siderophores, whereas the control strain showed decreased growth rate and increased siderophore production. Transcriptomic data revealed over 25 iron related genes with altered transcript levels. Results suggest MpkA is involved with regulation of broad cellular functions in the absence of stress.


Subject(s)
Aspergillus nidulans/genetics , Mitogen-Activated Protein Kinases/genetics , Phosphoproteins/genetics , Transcriptome/genetics , Aspergillus nidulans/enzymology , Aspergillus nidulans/growth & development , Cell Cycle Proteins/genetics , Cell Wall/genetics , Cell Wall/metabolism , Gene Expression Regulation, Fungal/genetics , Iron/metabolism , Sequence Deletion/genetics , Signal Transduction/genetics
10.
J Mol Diagn ; 21(2): 318-329, 2019 03.
Article in English | MEDLINE | ID: mdl-30610921

ABSTRACT

Orthogonal confirmation of next-generation sequencing (NGS)-detected germline variants is standard practice, although published studies have suggested that confirmation of the highest-quality calls may not always be necessary. The key question is how laboratories can establish criteria that consistently identify those NGS calls that require confirmation. Most prior studies addressing this question have had limitations: they have been generally of small scale, omitted statistical justification, and explored limited aspects of underlying data. The rigorous definition of criteria that separate high-accuracy NGS calls from those that may or may not be true remains a crucial issue. We analyzed five reference samples and over 80,000 patient specimens from two laboratories. Quality metrics were examined for approximately 200,000 NGS calls with orthogonal data, including 1662 false positives. A classification algorithm used these data to identify a battery of criteria that flag 100% of false positives as requiring confirmation (CI lower bound, 98.5% to 99.8%, depending on variant type) while minimizing the number of flagged true positives. These criteria identify false positives that the previously published criteria miss. Sampling analysis showed that smaller data sets resulted in less effective criteria. Our methodology for determining test- and laboratory-specific criteria can be generalized into a practical approach that can be used by laboratories to reduce the cost and time burdens of confirmation without affecting clinical accuracy.


Subject(s)
Genetic Testing/methods , High-Throughput Nucleotide Sequencing/methods , Algorithms , Genetic Variation/genetics , Humans , Sequence Analysis, DNA
11.
RSC Adv ; 9(37): 21075-21085, 2019 Jul 05.
Article in English | MEDLINE | ID: mdl-35521310

ABSTRACT

A biocompatible Dex-MA/PAA hydrogel was prepared through copolymerization of glycidyl methacrylate substituted dextran (Dex-MA) with acrylic acid (AA), which was applied as the adsorbent to remove cationic dyes from aqueous solutions. Dex-MA/PAA hydrogel presented a fast adsorption rate and the removal efficiency of Methylene Blue (MB) and Crystal Violet (CV) reached 93.9% and 86.4%, respectively within one minute at an initial concentration of 50 mg L-1. The adsorption equilibrium data fitted the Sips isotherm model well with high adsorption capacities of 1994 mg g-1 for MB and 2390 mg g-1 for CV. Besides, dye adsorption occurred efficiently over the pH range 3-10 and the temperature range 20-60 °C. Moreover, the removal efficiencies for MB and CV were still >95% even after five adsorption/desorption cycles which indicates the robust nature of the Dex-MA/PAA hydrogel and its potential as an eco-friendly adsorbent for water treatment.

12.
Genet Med ; 21(1): 114-123, 2019 01.
Article in English | MEDLINE | ID: mdl-29895855

ABSTRACT

PURPOSE: We investigated the frequencies and characteristics of intragenic copy-number variants (CNVs) in a deep sampling of disease genes associated with monogenic disorders. METHODS: Subsets of 1507 genes were tested using next-generation sequencing to simultaneously detect sequence variants and CNVs in >143,000 individuals referred for genetic testing. We analyzed CNVs in gene panels for hereditary cancer syndromes and cardiovascular, neurological, or pediatric disorders. RESULTS: Our analysis identified 2844 intragenic CNVs in 384 clinically tested genes. CNVs were observed in 1.9% of the entire cohort but in a disproportionately high fraction (9.8%) of individuals with a clinically significant result. CNVs accounted for 4.7-35% of pathogenic variants, depending on clinical specialty. Distinct patterns existed among CNVs in terms of copy number, location, exons affected, clinical classification, and genes affected. Separately, analysis of de-identified data for 599 genes unrelated to the clinical phenotype yielded 4054 CNVs. Most of these CNVs were novel rare events, present as duplications, and enriched in genes associated with recessive disorders or lacking loss-of-function mutational mechanisms. CONCLUSION: Universal intragenic CNV analysis adds substantial clinical sensitivity to genetic testing. Clinically relevant CNVs have distinct properties that distinguish them from CNVs contributing to normal variation in human disease genes.


Subject(s)
DNA Copy Number Variations/genetics , Genetic Association Studies , Genetic Diseases, Inborn/genetics , Genetic Predisposition to Disease , Comparative Genomic Hybridization , Exons/genetics , Genetic Diseases, Inborn/pathology , Genetic Testing , High-Throughput Nucleotide Sequencing , Humans , Phenotype
13.
Sci Rep ; 8(1): 11433, 2018 07 30.
Article in English | MEDLINE | ID: mdl-30061727

ABSTRACT

Filamentous fungi are widely used in the production of a variety of industrially relevant enzymes and proteins as they have the unique ability to secrete tremendous amounts of proteins. However, the secretory pathways in filamentous fungi are not completely understood. Here, we investigated the role of a mutation in the POlarity Defective (podB) gene on growth, protein secretion, and cell wall organization in Aspergillus nidulans using a temperature sensitive (Ts) mutant. At restrictive temperature, the mutation resulted in lack of biomass accumulation, but led to a significant increase in specific protein productivity. Proteomic analysis of the secretome showed that the relative abundance of 584 (out of 747 identified) proteins was altered due to the mutation. Of these, 517 were secreted at higher levels. Other phenotypic differences observed in the mutant include up-regulation of unfolded protein response (UPR), deformation of Golgi apparatus and uneven cell wall thickness. Furthermore, proteomic analysis of cell wall components in the mutant revealed the presence of intracellular proteins in higher abundance accompanied by lower levels of most cell wall proteins. Taken together, results from this study suggest the importance of PodB as a target when engineering fungal strains for enhanced secretion of valuable biomolecules.


Subject(s)
Aspergillus nidulans/cytology , Aspergillus nidulans/metabolism , Cell Wall/metabolism , Fungal Proteins/metabolism , Aspergillus nidulans/genetics , Aspergillus nidulans/growth & development , Cell Wall/ultrastructure , Fungal Proteins/genetics , Gene Expression Regulation, Fungal , Genotype , Hyphae/ultrastructure , Mutation/genetics , Phenotype , Proteomics , Temperature , Unfolded Protein Response , Up-Regulation
14.
Org Biomol Chem ; 16(34): 6206-6223, 2018 08 29.
Article in English | MEDLINE | ID: mdl-30106402

ABSTRACT

The effect of the degree of conformational rigidity and/or flexibility on preorganisation in artificial molecular receptors continues to be actively explored by supramolecular chemists. This work describes a bis-porphyrin architecture, linked via a rigid polycyclic backbone, in which a sterically bulky 2,3,5,6-tetramethylphenyl diimide core restricts rotation to afford two non-interconvertible tweezer conformations; syn- and anti-. After separation, the host-guest chemistry of each conformation was studied independently. The difference in host geometry allows only the syn-conformation to form a strong 1 : 1 bis-porphyrin complex with the diamino ligand 1,4-diazabicyclo[2.2.2]octane (DABCO) (K11 = 1.25 × 108 M-1), with the anti-conformation adopting a 2 : 2 sandwich complex with DABCO (K22 = 5.57 × 1017 M-3).

15.
Ann Surg Oncol ; 25(10): 2925-2931, 2018 Oct.
Article in English | MEDLINE | ID: mdl-29998407

ABSTRACT

BACKGROUND: An estimated 5-10% of breast and ovarian cancers are due to hereditary causes such as hereditary breast and ovarian cancer (HBOC) syndrome. Medicare, the third-party payer that covers 44 million patients in the United States, has implemented a set of clinical criteria to determine coverage for the testing of the BRCA1 and BRCA2 genes. These criteria, developed to identify carriers of BRCA1/2 variants, have not been evaluated in the panel testing era. This study investigated a series of Medicare patients undergoing genetic testing for HBOC to determine the efficacy of genetic testing criteria in identifying patients with hereditary risk. METHODS: This study retrospectively examined de-identified data from a consecutive series of Medicare patients undergoing genetic testing based on personal and family history of breast and gynecologic cancer. Ordering clinicians indicated whether patients did or did not meet established criteria for BRCA1/2 genetic testing. The genetic test results were compared between the group that met the criteria and the group that did not. Patients in families with known pathogenic (P) or likely pathogenic (LP) variants were excluded from the primary analysis. RESULTS: Among 4196 unique Medicare patients, the rate of P/LP variants for the patients who met the criteria for genetic testing was 10.5%, and for those who did not, the rate was 9% (p = 0.26). CONCLUSIONS: The results of this study indicate that a substantial number of Medicare patients with clinically actionable genetic variants are being missed by current testing criteria and suggest the need for significant expansion and simplification of the testing criteria for HBOC.


Subject(s)
Genetic Testing/standards , Hereditary Breast and Ovarian Cancer Syndrome/diagnosis , Hereditary Breast and Ovarian Cancer Syndrome/genetics , Adult , Aged , Aged, 80 and over , Diagnostic Errors , Female , Genes, BRCA1 , Genes, BRCA2 , Genetic Predisposition to Disease , Genetic Testing/methods , Humans , Male , Medicare , Middle Aged , Patient Selection , Retrospective Studies , Treatment Outcome , United States , Young Adult
16.
Microbiome ; 6(1): 86, 2018 05 10.
Article in English | MEDLINE | ID: mdl-29747692

ABSTRACT

BACKGROUND: As the importance of beneficial bacteria is better recognized, understanding the dynamics of symbioses becomes increasingly crucial. In many gut symbioses, it is essential to understand whether changes in host diet play a role in the persistence of the bacterial gut community. In this study, termites were fed six dietary sources and the microbial community was monitored over a 49-day period using 16S rRNA gene sequencing. A deep backpropagation artificial neural network (ANN) was used to learn how the six different lignocellulose food sources affected the temporal composition of the hindgut microbiota of the termite as well as taxon-taxon and taxon-substrate interactions. RESULTS: Shifts in the termite gut microbiota after diet change in each colony were observed using 16S rRNA gene sequencing and beta diversity analyses. The artificial neural network accurately predicted the relative abundances of taxa at random points in the temporal study and showed that low-abundant taxa maintain community driving correlations in the hindgut. CONCLUSIONS: This combinatorial approach utilizing 16S rRNA gene sequencing and deep learning revealed that low-abundant bacteria that often do not belong to the core community are drivers of the termite hindgut bacterial community composition.


Subject(s)
Bacteria/classification , Gastrointestinal Microbiome/genetics , Gastrointestinal Tract/microbiology , Isoptera/microbiology , Animals , Bacteria/genetics , Bacteria/isolation & purification , Base Sequence , DNA, Bacterial/genetics , Diet , Lignin/metabolism , Sequence Analysis, DNA , Symbiosis/physiology
17.
Cancer ; 124(8): 1691-1700, 2018 04 15.
Article in English | MEDLINE | ID: mdl-29360161

ABSTRACT

BACKGROUND: Approximately 10% of pancreatic adenocarcinoma (PC) cases are attributed to hereditary causes. Individuals with PC and a personal history of another cancer associated with hereditary breast and ovarian cancer (HBOC) or Lynch syndrome (LS) may be more likely to carry germline mutations. METHODS: Participants with PC and a history of cancer were selected from a pancreatic disease registry. Of 1296 individuals with PC, 149 had a relevant history of cancer. If banked DNA was available, a multigene panel was performed for individuals who had not 1) previously had a mutation identified through clinical testing or 2) undergone clinical multigene panel testing with no mutations detected. RESULTS: Twenty-two of 124 individuals with PC and another HBOC- or LS-related cancer who underwent genetic testing had a mutation identified in a PC susceptibility gene (18%). If prostate cancer is excluded, the mutation prevalence increased to 23% (21/93). Mutation carriers were more likely to have more than 1 previous cancer diagnosis (P = .001), to have had clinical genetic testing (P = .001), and to meet National Comprehensive Cancer Network (NCCN) genetic testing criteria (P < .001). Approximately 23% of mutation carriers did not meet NCCN HBOC or LS testing guidelines based on their personal cancer history and reported cancer history in first-degree relatives. CONCLUSION: At least 18% of individuals with PC and a personal history of other HBOC- or LS-related cancers carry mutations in a PC susceptibility gene based on our data, suggesting that criteria for genetic testing in individuals with PC should include consideration of previous cancer history. Cancer 2018;124:1691-700. © 2018 American Cancer Society.


Subject(s)
Biomarkers, Tumor/genetics , Germ-Line Mutation , Neoplasms, Second Primary/genetics , Pancreatic Neoplasms/genetics , Adolescent , Adult , Aged , Aged, 80 and over , Colorectal Neoplasms, Hereditary Nonpolyposis/genetics , DNA Mutational Analysis , Female , Genetic Predisposition to Disease , Hereditary Breast and Ovarian Cancer Syndrome/genetics , Humans , Male , Medical History Taking , Middle Aged , Young Adult , Pancreatic Neoplasms
18.
Proc Natl Acad Sci U S A ; 115(2): 379-384, 2018 01 09.
Article in English | MEDLINE | ID: mdl-29279374

ABSTRACT

A major challenge in evaluating the contribution of rare variants to complex disease is identifying enough copies of the rare alleles to permit informative statistical analysis. To investigate the contribution of rare variants to the risk of type 2 diabetes (T2D) and related traits, we performed deep whole-genome analysis of 1,034 members of 20 large Mexican-American families with high prevalence of T2D. If rare variants of large effect accounted for much of the diabetes risk in these families, our experiment was powered to detect association. Using gene expression data on 21,677 transcripts for 643 pedigree members, we identified evidence for large-effect rare-variant cis-expression quantitative trait loci that could not be detected in population studies, validating our approach. However, we did not identify any rare variants of large effect associated with T2D, or the related traits of fasting glucose and insulin, suggesting that large-effect rare variants account for only a modest fraction of the genetic risk of these traits in this sample of families. Reliable identification of large-effect rare variants will require larger samples of extended pedigrees or different study designs that further enrich for such variants.


Subject(s)
Diabetes Mellitus, Type 2/genetics , Genetic Predisposition to Disease/genetics , Genetic Variation , Mexican Americans/genetics , Diabetes Mellitus, Type 2/ethnology , Diabetes Mellitus, Type 2/pathology , Family Health , Female , Gene Frequency , Genetic Predisposition to Disease/ethnology , Genome-Wide Association Study/methods , Genotype , Humans , Male , Pedigree , Phenotype , Quantitative Trait Loci/genetics , Whole Genome Sequencing/methods
19.
Genet Med ; 20(2): 282, 2018 02.
Article in English | MEDLINE | ID: mdl-29215652

ABSTRACT

This corrects the article DOI: 10.1038/gim.2017.60.

20.
J Mol Diagn ; 20(1): 4-27, 2018 01.
Article in English | MEDLINE | ID: mdl-29154853

ABSTRACT

Bioinformatics pipelines are an integral component of next-generation sequencing (NGS). Processing raw sequence data to detect genomic alterations has significant impact on disease management and patient care. Because of the lack of published guidance, there is currently a high degree of variability in how members of the global molecular genetics and pathology community establish and validate bioinformatics pipelines. Improperly developed, validated, and/or monitored pipelines may generate inaccurate results that may have negative consequences for patient care. To address this unmet need, the Association of Molecular Pathology, with organizational representation from the College of American Pathologists and the American Medical Informatics Association, has developed a set of 17 best practice consensus recommendations for the validation of clinical NGS bioinformatics pipelines. Recommendations include practical guidance for laboratories regarding NGS bioinformatics pipeline design, development, and operation, with additional emphasis on the role of a properly trained and qualified molecular professional to achieve optimal NGS testing quality.


Subject(s)
Computational Biology/standards , Guidelines as Topic , High-Throughput Nucleotide Sequencing/standards , Pathology, Molecular/standards , Humans , Laboratories , Reproducibility of Results , United States
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