Deoxyribonucleic Acid Mutation Research Articles

Fragmentation patterns of cell-free DNA and somatic mutations in the urine of metastatic breast cancer patients.

Urinary cell-free deoxyribonucleic acid (DNA) (ucfDNA) holds promise as a biomarker; however, its potential remains largely unexplored. We examined the fragmentation pattern of ucfDNA and identified somatic mutations within urine samples from metastatic breast cancer (MBC) patients. Urine and blood specimens were collected before treatment from 45 MBC patients and posttreatment urine samples from 16 of the 45 patients at the China National Cancer Center. Somatic mutations and tumor mutational burden (TMB) in the urine and plasma of 10 patients were analyzed by next-generation sequencing (NGS). Fragmentation patterns of cfDNA were displayed using electropherograms. Differences in the extracted amount of cfDNA, length of cfDNA fragments, and TMB between urine and plasma were compared using a Wilcoxon test. The fragmentation patterns of ucfDNA were categorized as follows: (1) profile A (n = 26) containing a short peak (100-200 bp) and a long peak (>1500 bp); (2) profile B (n = 8) containing only a long peak; and (3) profile C (n = 11) containing flat pattern. For profile A patients, the short-peaked ucfDNA circulating in the bloodstream was much shorter compared with plasma cfDNA (149 vs. 171 bp, Wilcoxon test, P = 0.023). The fragmentation patterns in lung metastasis patients exhibited a higher propensity toward profile C ( P = 0.002). After treatment, 87.5% of the patients exhibited consistent fragmentation patterns. The concordance rate for somatic mutations in the plasma and urine was 30%, and the median TMB of urine and plasma was not significantly different. This study established a fragmentation pattern for ucfDNA and detected somatic mutations in the urine of MBC patients. These results suggest the potential application of ucfDNA as a biomarker for MBC.

Biophysical model for DNA mutations induced by retroviral genome insertion based on the probability density function of mutation distribution

Research into the biophysical properties of deoxyribonucleic acid (DNA) and the mechanisms underlying genetic mutations has undergone marked advancements. The intriguing nature of mutations resulting from retroviral DNA insertion has garnered considerable attention. Whether these mutations are random or region-specific, the distribution patterns of mutation sites have been the focus of numerous research endeavours. This mutation mechanism originates from interactions between host DNA and the pre-integration complex (PIC), comprising retroviral DNA and an integrase enzyme that facilitates its incorporation into the host DNA. Our study focused on the Zfp521 gene locus, recognised for its pronounced susceptibility to insertional mutations, particularly around unique palindromic sequences. We employed two biophysical models to predict mutation distribution within a range of 50 base pairs centred on these sequences. The first is a probabilistic collision model emphasising PIC and target DNA interactions. The second model is a DNA diffraction lattice, where the PIC behaves according to probability density. Although both models adeptly illuminated the probability distributions of target sites, the second model was more successful in predicting the PIC integration sites based on DNA biophysical properties. This highlights the pivotal role of intricate interactions between the PIC and target DNA, suggesting that mutations can be predicted in a stochastic manner.

SKIN CANCER IN CHILDREN WITH XERODERMA PIGMENTOSUM

Introduction: Xeroderma pigmentosum) is a rare disease, inherited in an autosomal recessive manner with disturbances in the repair of deoxyribonucleic acid (DNA) which often occur in malignancy. Irreversible DNA lesions and mutations also occur in the genes which regulate skin cancer development in Xeroderma Pigmentosum. Purpose: To explain the signs, symptoms, and management of skin cancer Xeroderma Pigmentosum. Case Report : A 6 year old girl with basal cell carcinoma arising from Xeroderma pigmentosum. The histopathological picture of the left nasolabial biopsy preparation was found to show basal cell carcinoma (BCC). The patient was treated with 5FU administration and were followed after 6 week In the second patient, a 3 year old boy, squamous cell carcinoma in the oocipital area. From the histopathological picture, moderately differentiated squamous cell carcinoma on the left frontalis occipital dextra and corresponds to mottled hypermegrance on the parietal dextra. In this patient, a wide excision of the occipital lump was performed and the defect was closed with a full-thickness skin graft. Provided education to the parents of both patients for direct prevention of sun exposure by using sunscreen/hats. Discussion and Conclusion: Xeroderma Pigmentosum patients who are Xeroderma Pigmentosum to ultraviolet radiation (UV) can result in the development of highly cancerous lesions consisting of squamous cell carcinoma (SCC), basal cell carcinoma (BCC), and malignant melanoma (MM). Clinical management of Xeroderma Pigmentosum includes sun avoidance, minimizing UV eXeroderma Pigmentosumosure, early detection, skin lesions, and genetic counseling. Topical application of 5-fluorouracil or imiquimod is used for premalignant lesions, and surgical excision is performed for malignant neoplasms of the skin, tongue, eyelids, conjunctiva, and cornea.

S2096 PALB2 and the Risk for Colorectal Cancer

Introduction: Colorectal cancer (CRC) is the most prevalent cancer in the gastrointestinal system and the third leading cause of cancer-related deaths in the United States. Hereditary factors play an important role in the risk of CRC and it has been estimated that up to 30% of CRC cases are affected by genetic factors. However, mutations in CRC-susceptibility genes explain less than 10% of CRC cases. Germline mutations in deoxyribonucleic acid (DNA)-repair genes have recently been reported more frequently in CRC. PALB2 is one such germline mutation that was recently evidenced as a CRC risk gene. We present a case of a female patient diagnosed with invasive sigmoid adenocarcinoma in the setting of no significant risk factors except for positive gene testing for PALB2. Case Description/Methods: A 32-year-old female with no significant past medical history presented with an episode of painless, large-volume bright red blood per rectum. She endorsed a 2-month history of intermittent rectal bleeding noted on wiping. Complete blood count revealed a microcytic anemia with hemoglobin of 8.4. Iron panel was consistent with anemia of chronic disease. Colonoscopy revealed a large, infiltrating and partially obstructing mass in the recto-sigmoid colon measuring 6 cm with evidence of mucosal bleeding. Biopsy confirmed invasive adenocarcinoma. Computed tomography (CT) of the abdomen showed multiple hypodense hepatic lesions suggestive of metastatic disease (Figure 1). Discussion: Mutations in PALB2 have been associated with an increased risk of familial cancers including breast, pancreatic, and gastric cancers. PALB2 encodes a protein that functions in tumor suppression and is primarily involved in the DNA repair process. PALB2 is altered in 2.8% of colorectal cancer cases. One study proved that PALB2 was an independent prognostic factor in CRC. Further studies on mutations involving PALB2 in CRC can help delineate a patient’s risk for malignancy and provide vital information for gastric cancer prevention. It will also allow for more personalized treatment options to have improved survival outcomes.Figure 1.: Malignant, partially obstructing tumor in the recto-sigmoid colon that was about 19 to 25 cm from the anal verge.

P432 Detection of erg11 gene mutation in fluconazole resistant Candida albicans isolates

Poster session 3, September 23, 2022, 12:30 PM - 1:30 PMObjectiveTo determine the profile of fluconazole-resistant Candida isolates (FRCS) and the proportion of erg11 gene mutation in fluconazole-resistant C. albicans (FRCA) isolatesMethodsAfter getting approval from ethics the study was conducted on 150 isolates of FRCS obtained from patients admitted to our tertiary care hospital from September 2019 to December 2021. All the isolates were revived onto Sabouraud dextrose agar (SDA) and identified by Matrix-Assisted Laser Desorption/Ionization-Time of Flight Mass Spectrometry (MALDI-TOF MS). Fluconazole-resistance was detected by VITEK 2 automated system. Deoxyribonucleic acid (DNA) of FRCA isolates were extracted by QIAamp DNA Mini kit (Qiagen-51 304, Hilden, Germany) as per manufacturer's instruction. A single primer pair targeting the nucleotide sequence from 1067 to 1576 bp region of erg11 gene was used for amplification as per Xu et al. with minor modification and 500 bp polymerase chain reaction (PCR) products were observed by gel electrophoresis. A positive clinical isolate of FRCA was used as a positive control. The PCR products were purified and subjected to Sanger sequencing with an ABI PRISM DNA analyzer (Applied Biosystems) and mutations were detected by using Mega (version 7) software by comparing with the published GenBank sequence AF153844.1 of C. albicans strain ATCC 28516. Categorical variables were expressed in percentages and continuous variables were expressed in mean (average).ResultsOut of the total of 150 FRCS, the most common fluconazole-resistant agent of candidiasis was C. auris, which was isolated from 60 (40%) cases followed by 24 (16%) isolates of C. glabrata, 19 (12.7%) isolates of C. krusei, 18 (12%) isolates of C. parapsilosis, 17 (11.3%) isolates of C. albicans, 10 (6.7%) isolates of C. tropicalis, and only two (1.3%) isolates of C. guilliermondii. Among these 17 FRCA isolates, 9 isolates were obtained from genital swabs, 5 from blood, and a single isolate each from the perianal swab, ear swab, and sputum. A total of 12 (70.6%) out of 17 FRCA isolates yielded 500 bp region in erg11 gene. Gel electrophoresis image of PCR products of erg11 gene is depicted in Figure 1. Sequencing of these products detected a single missense mutation A1309G (V437I) in one FRCA isolate. Most of the FRCA isolates had an average of 4 silent mutations (observed in 6 isolates) and a single isolate had 6 silent mutations. A total of 8 different silent mutations were observed among FRCA isolates T1296C (83.3%), C1203T (66.7%), A1440G (66.7%), C1302T (50%), T1470C (50%), T1140C (25%), T1110C (16.7%), and T1284C (8.3%).Conclusion C. auris was the most common fluconazole resistant isolate observed, followed by C. glabrata, C. krusei, C. parapsilosis, C. albicans, C. tropicalis, and C. guilliermondii. There were many silent mutations observed in erg11 gene of FRCA isolates and detected only a single missense mutation (V437I). Fluconazole-resistant in FRCA isolates may be due to mechanisms other than the studied one in our region.

Facial skin ageing: Key concepts and overview of processes.

IntroductionThe face is a cosmetically sensitive region where the process of ageing is most clearly manifested. With increased focus on anti‐ageing and longevity, more anti‐senescent treatments are being proposed despite limited evidence. This study outlines the pathways and mechanisms underpinning the biological process of ageing in the face.MethodsComprehensive searches of MEDLINE, EMBASE, Cochrane Library and CINAHL from inception to 2020. Inclusion criteria included all empirical human research studies specific to facial ageing features, written in the English language.ResultsA total of 65 papers met inclusion criteria for analysis. Pathways were subdivided into intrinsic and extrinsic senescence mechanisms. Intrinsic pathways included genetics, generation of reactive oxygen species and hormonal changes. Extrinsic pathways included photoageing and damage to skin layers. The combined intrinsic and extrinsic pathway alterations result in wrinkles, higher laxity, slackness and thinning of the skin. Skin functions such as barrier immune function, wound healing, thermoregulation and sensory function are also impaired.ConclusionThe ageing process is unique to the individual and depends on the interplay between an individual's genetics and external environmental factors. Through understanding the molecular and cellular mechanisms, an appreciation of the consequent structural and functional changes can be achieved. Based on this knowledge, further research can focus on how to slow or impede the ageing process and identify specific targets to develop and evolve new treatment strategies.

Early dynamics of circulating tumor DNA predict clinical response to immune checkpoint inhibitors in metastatic renal cell carcinoma.

ObjectivesDetection of genomic alterations in circulating tumor deoxyribonucleic acid of peripheral blood can guide the selection of systemic therapy in cancer patients. The predictive significance of circulating tumor deoxyribonucleic acid in metastatic renal cell carcinoma remains unclear, especially for patients treated with immune checkpoint inhibitors.MethodsIn this study, we collected plasma samples before and 1 month after commencing nivolumab monotherapy or nivolumab plus ipilimumab therapy from 14 metastatic renal cell carcinoma patients. We performed circulating tumor deoxyribonucleic acid genomic profiling in plasma cell‐free deoxyribonucleic acid by next‐generation sequencing using a commercially available pan‐cancer panel (Guardant360 CDx). Additionally, we also performed whole exome sequencing of tumor tissues and compared the concordance of genomic profiles with circulating tumor deoxyribonucleic acid.ResultsNine patients had circulating tumor deoxyribonucleic acid in pretreatment plasma samples with a total of 20 mutations (15 single nucleotide variants, three insertions/deletions, and two copy number amplification). VHL (30.0%) was the most frequently mutated gene, followed by TP53 (20.0%), and 45.0% of circulating tumor deoxyribonucleic acid mutations were concordant with somatic mutations in tumor tissues. Patients with decreasing circulating tumor deoxyribonucleic acid mutant allele frequency had better progression free survival when compared to those with increasing mutant allele frequency (P = 0.0441).ConclusionsOur findings revealed that early circulating tumor deoxyribonucleic acid dynamics can serve as a predictive biomarker for response to immune checkpoint inhibitors in metastatic renal cell carcinoma patients.

Statistical mechanics of DNA mutation using SUSY quantum mechanics

This paper investigates the deoxyribonucleic acid (DNA) denaturation through statistical mechanics and demonstrates that the exceptional polynomials lead to DNA mutation. A DNA model with two chains connected by the Morse potential representing the H bonds is considered and the partition function for this model is computed. The partition function is converted into a Schrödinger-like equation. The techniques of SUSY quantum mechanics are used to model the DNA mutation. The thermal denaturation of DNA for each mutated state is also computed.

A theoretical study on the role of stability of cytosine and its tautomers in DNA (deoxyribonucleic acid), and investigation of interactions of Na+, K+, Mg2+, Ca2+, Zn2+ metal ions and OH radical with cytosine tautomers

In the present study, 21 cytosine tautomers were investigated so that some tautomers were reported for the first time in the gas phase and aqueous solution. C3 tautomer was the most stable tautomer in gas phase but C1 was the most stable structure in aqueous solution. The potential energy surface of all trajectories was determined for 21 tautomers and 22 transition states. Also, interactions of cytosine tautomers with Na+, K+, Mg2+, Ca2+ and Zn2+ metal ions were studied in gas phase and aqueous solution. Three types of interactions among metal ions and (N1 and O10), (N3 and O10) and (N3 and N9) of cytosine tautomers were investigated. The study of interaction energies of all complexes showed the stability of complexes in which interactions among Mg2+ and Zn2+ with tautomers were stronger than interactions among Ca2+, Na+ and K+ with tautomers, respectively. Some interactions of metal ions with cytosine tautomers made the most stable tautomers. So, the stability of rare tutomeric forms had a significant effect on stabilization of anomalous DNA (deoxyribonucleic acid) double helix and spontaneous mutations. Also, one of the most important causes of mutations in DNA (deoxyribonucleic acid) was the reaction of OH radical with nucleotide bases. So, interactions of OH radical with cytosine and its tautomers were investigated in gas phase and aqueous solution. Communicated by Ramaswamy H. Sarma

Cochlear implant in Kearns-Sayre syndrome: A case study of twin sisters

<p>Hearing loss may be related to several factors, including hearing loss resulting from certain genetic syndromes. Kearns-Sayre syndrome is characterized by mutations in mitochondrial DNA (deoxyribonucleic acid), responsible for the production of energy (adenosine triphosphate-ATP), which is extremely important for the development of structures that require it, such as the cochlea. The case was followed up at the hospital since 2000, due to the progressive characteristic of hearing loss found in audiological tests and findings in cases related to the syndrome. The intervention with individual sound amplification devices proved to be of little benefit for good oral communication of one of the patients, who was diagnosed with bilateral profound hearing loss. Thus, after discussions in clinical meetings, the team opted for the indication of the cochlear implant for the patient, according to the current criteria for indication of this surgery, and with which it obtained good results. His twin sister, who presented good results with hearing aids, will continue in audiological follow-up, to verify the evolution of the case and discuss a new approach, if necessary. Patients with suspected or diagnosed Kearns-Sayre syndrome should seek audiological diagnosis, because it is a possible progressive hearing loss, requiring rehabilitation with the use of hearing devices. Maintaining oral communication is extremely important because, in these cases, other functions will be impaired, such as muscle tone and vision.</p>

PHENOTYPIC AND GENOTYPIC CHARACTERIZATION OF FLUOROQUINOLONE DRUG RESISTANCE AMONG STAPHYLOCOCCUS AUREUS IN A TERTIARY CARE HOSPITAL

Objective: The objective of the study was to determine whether recent use of topical fluoroquinolones is a risk factor for in vitro fluoroquinolone resistance in Staphylococcus aureus ocular isolates. Fluoroquinolone antibiotics such as ciprofloxacin (CIP) are useful drugs against infections caused by Staphylococcus aureus and mutations in deoxyribonucleic acid (DNA) gyrase which control bacterial DNA topology, can be one of the reasons of occurrence resistance to this class of antibiotics. Therefore, finding new mutations and study of the quinolone interaction with mutated GyrA can provide important issues for explanation resistance.
 Methods: Bacterial identification was confirmed by appropriate morphological, cultural, and biochemical tests. The antibiotic susceptibility pattern was determined for all isolates. The possible involvement of efflux pumps in mediating fluoroquinolone resistance as well as changes in the quinolone resistance-determining region (QRDR) of gyrA gene was investigated.
 Results: Differences in methicillin resistance among staphylococci were observed based on patient age, with higher rates observed in older patients (p<0.0001). Out of 91 isolates, 77 (84.61%) were resistant to CIP and 47 (51.65%) were resistant to ofloxacin (OF). Confirmation with agar dilution test showed that 57 samples were resistant to CIP, 38 samples were resistant to OF, and 29 samples were resistant to both CIP and OF. By polymerase chain reaction (PCR) testing, gyrA genes in resistance strains were amplified. All the five resistant isolates were found to be positive for the presence of a fluoroquinolones resistance gene (gyrA gene) and the two sensitive isolates were found to be negative. Resistance among CIP and OF in isolated harboring a mutation GyrA was of statistical significance among S. aureus (p<0.001).
 Conclusion: The result of this study will be useful to update the antibiotic policy in our hospital set up and controlling the irrational use of antibiotics among health care workers. The information obtained will provide a baseline data that can be used to design further research for prevention of drug resistance caused by Staphylococcus aureus.

SUN-155 A Complex Case of Adrenal Insufficiency Associated with NLRP1 Gene Mutation in a Patient with Myopathy and Mitochondrial Cytopathy

Most cases of Addison’s disease are due to an autoimmune response, with the most commonly associated genes belonging to human leukocyte antigen (HLA) complex. Genome wide association studies have shown a significant association of variants of Nuclear Localization Leucine-Rich-Repeat Protein 1 (NLRP1) with Addison’s disease. NLRP1 protein is involved in the assembly of inflammasome which promotes the secretion of interleukin-1β, interleukin-18 and downstream inflammatory responses to regulate inflammation. With underlying myopathy and mitochondrial disease, coexisting adrenal insufficiency may be challenging to identify. A 36-year-old female presented for evaluation of fatigue, myalgia, and dyspnea for several years. She carried a diagnosis of asthma, myopathy, gastroparesis requiring a gastric stimulator, and recently diagnosed adrenal insufficiency secondary to long term fluticasone use. Beside low blood pressure of 91/64 millimetres of mercury, physical exam was unremarkable. Lab findings were significant for dehydroepiandrosterone-sulfate (DHEAS) of 7.0 micrograms per deciliter (mcg/dL), Adrenocorticotropic hormone (ACTH) of 7.2 picograms per milliliter and cortisol of 1.4 mcg/dL. Adrenal insufficiency was confirmed with cosyntropin stimulation test. Methacholine challenge test showed worsening asthma. She was managed with empiric stress dose steroids when indicated. Muscle fatigue progressed despite taking ubiquinol, B100 and carnitine. She was further evaluated with muscle biopsy that showed type two fiber atrophy. Muscle coenzyme Q10 was 0.08 mcg/dL, and citrate synthase was 50% of normal, insufficient for electron transport complex I. Whole exome sequencing showed mutations in NLRP1 in addition to Myosin Heavy Chain 2 (MYH2) and Sodium voltage-gated Channel alpha subunit 4 (SCN4a) both of which are associated with myopathy. She was then started on a short-acting glucocorticoid regimen. While her adrenal insufficiency was initially thought to be secondary to inhaled steroids, subsequent mutation analysis suggested that she was prone to autoimmunity. This case illustrates the association of adrenal insufficiency with NLRP1 mutation. Furthermore, the symptoms of adrenal insufficiency and myopathy can overlap making it difficult to delineate. While so far most studies have dealt with mitochondrial myopathies due to deletions or point mutations in the mitochondrial deoxyribonucleic acid (DNA), a new field of investigation is that of syndromes due to mutations in the nuclear DNA.

An Efficient and Rapid Method for Detection of Mutations in Deoxyribonucleic Acid - Sequences

The comparison of genomic sequences plays a key role in determining the structural and functional relationships between genes. This comparison is carried out by identifying the similarities, differences and mutations between genomic sequences. This makes it possible to study and analyze the genetic and the evolutionary relationships between organisms. Alignment algorithms have been in the spotlight for the last few decades, due to a vast genomic data explosion. They have attracted a great deal of interest from many researchers who focus on the development of practical solutions to ensure effective alignments with an optimal response time. In this paper, a novel algorithm based on Discrete To Continuous "DTC" approach has been developed. The proposed methodology was compared against other existing methods, which are largely based on the concept of string matching. Experimental results show that the DTC algorithm delivers supremely efficient alignment with a reduced response time.

Persistence of Human Immunodeficiency Virus-1 Drug Resistance Mutations in Proviral Deoxyribonucleic Acid After Virologic Failure of Efavirenz-Containing Antiretroviral Regimens.

BackgroundEfavirenz (EFV)-based regimens select broad drug resistance to nonnucleoside reverse-transcriptase inhibitors (NNRTIs), limiting the effectiveness of EFV and other NNRTIs. The duration, persistence, and decay of drug resistance mutations (DRMs) in the proviral reservoir is not well defined.MethodsParticipants with virologic failure of EFV-based regimens and drug-resistant viremia with the K103N mutation in plasma ribonucleic acid (RNA) were identified from AIDS Clinical Trials Group (ACTG) studies A364 and A5095. These individuals received a second-line, boosted protease inhibitor-based regimen with suppression of viremia for up to10 years during long-term follow-up (median = 3.6 years; interquartile range, 2.1–6.9 years). Proviral deoxyribonucleic acid (DNA) from cryopreserved peripheral blood mononuclear cells was sequenced to identify the persistence of DRM.ResultsTwenty-eight participants from ACTG 364 and ACTG 5095 were evaluated. Sanger sequencing of proviral DNA detected K103N as well as additional reverse-transcriptase inhibitor (RTI) mutations. Ultradeep sequencing confirmed persistence of K103N in 71% of participants with minimal decay over time. In an adjusted model including years since suppression, persistent proviral K103N was 2.6 times more likely (95% confidence interval, 1.0–6.4) per log10 higher human immunodeficiency virus RNA at EFV failure.ConclusionsPersistence of RTI mutations in proviral DNA after virologic failure has implications for the effectiveness of future drug regimens and the recycling of RTI drugs.

Modeling and Analysis of Protein Synthesis and DNA Mutation Using Colored Petri Nets

In molecular biology, protein synthesis is an essential biological process of generating specific proteins in living systems. Many mathematical models are designed to characterize the process of the flow of genetic information from deoxyribonucleic acid (DNA) to protein; however, most of them cannot provide detailed and observed steps to describe and analyze this fundamental biological process. Colored Petri Net (CPN), as a mathematical method widely applied in the process analysis of discrete event dynamic systems, has increasingly become an innovative and efficient theoretical approach for exploring the biological processes. Aiming at describing the entire process of protein synthesis, a CPN-based model has been designed that successfully and intuitively represents the flow of genetic information involving transcription and translation. DNA mutations are permanent alterations in the nucleotide sequence of the DNA strand, while different types of mutations have various effects on the synthesized proteins. Based on the proposed protein synthesis model, we put forward a new CPN model to identify the type of mutation, which is beneficial for analyzing whether the mutation has impacts on the structure or function of the produced protein. The mutation position and bases mutated rate are obtained by contrasting the nucleobases on DNA sequences, while the mutation type is determined via the alignment of the amino acids in the polypeptide chain. The model’s effectiveness and accuracy are illustrated by biological mutation examples, indicating this method offers great superiority in modeling and analyzing the complex biological processes.

Molecular testing for Lynch syndrome in people with colorectal cancer: systematic reviews and economic evaluation.

Inherited mutations in deoxyribonucleic acid (DNA) mismatch repair (MMR) genes lead to an increased risk of colorectal cancer (CRC), gynaecological cancers and other cancers, known as Lynch syndrome (LS). Risk-reducing interventions can be offered to individuals with known LS-causing mutations. The mutations can be identified by comprehensive testing of the MMR genes, but this would be prohibitively expensive in the general population. Tumour-based tests - microsatellite instability (MSI) and MMR immunohistochemistry (IHC) - are used in CRC patients to identify individuals at high risk of LS for genetic testing. MLH1 (MutL homologue 1) promoter methylation and BRAF V600E testing can be conducted on tumour material to rule out certain sporadic cancers. To investigate whether testing for LS in CRC patients using MSI or IHC (with or without MLH1 promoter methylation testing and BRAF V600E testing) is clinically effective (in terms of identifying Lynch syndrome and improving outcomes for patients) and represents a cost-effective use of NHS resources. Systematic reviews were conducted of the published literature on diagnostic test accuracy studies of MSI and/or IHC testing for LS, end-to-end studies of screening for LS in CRC patients and economic evaluations of screening for LS in CRC patients. A model-based economic evaluation was conducted to extrapolate long-term outcomes from the results of the diagnostic test accuracy review. The model was extended from a model previously developed by the authors. Ten studies were identified that evaluated the diagnostic test accuracy of MSI and/or IHC testing for identifying LS in CRC patients. For MSI testing, sensitivity ranged from 66.7% to 100.0% and specificity ranged from 61.1% to 92.5%. For IHC, sensitivity ranged from 80.8% to 100.0% and specificity ranged from 80.5% to 91.9%. When tumours showing low levels of MSI were treated as a positive result, the sensitivity of MSI testing increased but specificity fell. No end-to-end studies of screening for LS in CRC patients were identified. Nine economic evaluations of screening for LS in CRC were identified. None of the included studies fully matched the decision problem and hence a new economic evaluation was required. The base-case results in the economic evaluation suggest that screening for LS in CRC patients using IHC, BRAF V600E and MLH1 promoter methylation testing would be cost-effective at a threshold of £20,000 per quality-adjusted life-year (QALY). The incremental cost-effectiveness ratio for this strategy was £11,008 per QALY compared with no screening. Screening without tumour tests is not predicted to be cost-effective. Most of the diagnostic test accuracy studies identified were rated as having a risk of bias or were conducted in unrepresentative samples. There was no direct evidence that screening improves long-term outcomes. No probabilistic sensitivity analysis was conducted. Systematic review evidence suggests that MSI- and IHC-based testing can be used to identify LS in CRC patients, although there was heterogeneity in the methods used in the studies identified and the results of the studies. There was no high-quality empirical evidence that screening improves long-term outcomes and so an evidence linkage approach using modelling was necessary. Key determinants of whether or not screening is cost-effective are the accuracy of tumour-based tests, CRC risk without surveillance, the number of relatives identified for cascade testing, colonoscopic surveillance effectiveness and the acceptance of genetic testing. Future work should investigate screening for more causes of hereditary CRC and screening for LS in endometrial cancer patients. This study is registered as PROSPERO CRD42016033879. The National Institute for Health Research Health Technology Assessment programme.

Mitochondrial mutations in patients with congenital heart defects by next generation sequencing technology

It has been shown that mitochondrial deoxyribo nucleic acid mutations may play an important role in the development of cardiomyopathy, and various types of cardiomyopathy can be attributed to disturbed mitochondrial oxidative energy metabolism. Several studies have described many mutations in mitochondrial genes encoding for subunits of respiratory chain complexes. Thus, recent studies confirm that pathologic mitochondrial deoxyribo nucleic acid mutations are a major reason of diseases and determining them by next-generation sequencing will improve our understanding of dysregulation of heart development. To analyse mitochondrial deoxyribo nucleic acid mutations, the entire mitochondrial deoxyribo nucleic acid was amplified in two overlapping polymerase chain reaction fragments from the cardiac tissue of the 22 patients with congenital heart disease, undergoing cardiac surgery. Mitochondrial deoxyribo nucleic acid was deep sequenced by next-generation sequencing. A total of 13 novel mitochondrial deoxyribo nucleic acid mutations were identified in nine patients. Of the patients, three have novel mutations together with reported cardiomyopathy mutations. In all, 65 mutations were found, and 13 of them were unreported. This study represents the most comprehensive mitochondrial deoxyribo nucleic acid mutational analysis in patients with congenital heart disease.

Early acute pancreatitis in a child with compound heterozygosis ∆F508/R1438W/Y1032C cystic fibrosis: a case report

IntroductionRecent studies suggest an important role of the cystic fibrosis transmembrane conductance regulator gene in the development of pancreatitis. It occurs approximately in 20% of patients with cystic fibrosis and almost exclusively in pancreatic sufficient people. Newborn screening and improved panels of deoxyribonucleic acid mutation analysis techniques are revealing more rare and nonclassical pictures of the disease, generally associated with pancreatic sufficiency and with an increased risk of developing pancreatitis. Mutations R1438 and Y1032 are considered rare mutations, and, when singularly associated with ∆F508, lead to a mild phenotype with pancreatic sufficiency and no detectable respiratory involvement.Case presentationWe present the case of a Caucasian girl, aged six years, whose genotype was characterized by three different mutations ∆F508, R1438W and Y1032C, never reported, together, in the same patient. She presented with a positive immunoreactive trypsinogen screening, a borderline sweat test, and, in the first years, a favorable pulmonary course, and pancreatic sufficiency. At the age of six years, she presented with a sudden episode of acute abdominal pain, anorexia and fever. A diagnosis of pancreatitis was made after clinical and laboratory examinations. Venous rehydration, bowel rest and therapy with ursodeoxycholic acid resulted in complete remission.The treatment was successful, with normalization of her symptoms and laboratory parameters within four weeks.ConclusionThere has been a vast expansion in the understanding of the wide range of phenotypes associated with cystic fibrosis transmembrane conductance regulator dysfunction since the discovery of the cystic fibrosis transmembrane conductance regulator gene. The genotype-phenotype correlation in pancreatitis is rare compared to other organ manifestations, since this is seen almost exclusively among pancreatic sufficient patients with cystic fibrosis. Our study supports that compound heterozygosis ∆F508-R1438W/Y1032C is a 'cystic fibrosis-causing genotype' characterized by an immunoreactive trypsinogen positive screening, abnormal sweat chloride testing, and pancreatic sufficiency, with an increased risk of acute pancreatitis at an early age.

Association of mitochondrial deoxyribonucleic acid mutation with polymorphism in CYP2E1 gene in oral carcinogenesis

Oral carcinogenesis is a complex process affected by genetic as well as environmental factors. CYP2E1 gene is involved in metabolism of number of compounds and carcinogens. Its normal functioning is required for homeostasis of free radical. Mitochondrial deoxyribonucleic acid (mtDNA) is 10-100 times more susceptible to damage than nuclear DNA. Mitochondrial DNA large scale deletions are well documented in oral cancer. However, the relationship between CYP2E1 gene polymorphisms and mtDNA damage is still not documented in literature. Case-control study involving 50 subjects was carried out. Deoxyribonucleic acid extraction was done from study subject tissue samples. Restriction fragment length polymorphism (RFLP) and polymerase chain reaction (PCR) amplification was done to confirm CYP2E1 gene polymorphisms. The PCR amplification was done for mtDNA 4977 bp deletion. Statistical analysis was carried out using SPSS version 11.5 with χ(2) tests. c1c1 and DD polymorphisms are prevalent in North Indian population having oral cancer. These polymorphisms are significantly associated with mtDNA 4977 bp deletion. Mitochondrial DNA damage induced by wild CYP2E1 forms and imperfect DNA repair in mtDNA may act synergistically to greatly enhance oral cancer risk.

Diagnosis and Management of Lynch Syndrome

Lynch syndrome (LS), or hereditary nonpolyposis colorectal cancer (HNPCC), represents 2% - 4% of all cases of colorectal cancer. LS is an autosomal-dominant inherited cancer predisposition syndrome caused by germline mutations in deoxyribonucleic acid (DNA) mismatch repair genes. Since the discovery of the major human genes with DNA mismatch repair function, mutations in five of them have been correlated with susceptibility to LS: mutS homolog 2 (MSH2); mutL homolog 1 (MLH1); mutS homolog 6 (MSH6); postmeiotic segregation increased 2 (PMS2); and postmeiotic segregation increased 1 (PMS1). The diagnostic features of LS have accumulated and been refined over time. Today, LS is defined by a set of clinical, pathological, and molecular features that encompass: a family history of colorectal cancer, a particular spectrum of extracolonic neoplasms, multiple colorectal tumors, early onset of cancer, particular histological features among colorectal cancers, presence of DNA microsatellite instability, loss of expression of DNA mismatch repair proteins, and germline mutation in a DNA mismatch repair gene. This review provides an overview of the diagnosis and management of LS patients, including some recently reported patents.