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Chen X, Xu Z, Lei X, Liang H, Wu F, Chen R, Guo Y, Xiong L. Amplicon sequencing-based carrier screening for 170 monogenic disorders among children with abnormal LC-MS/MS results. Clin Chim Acta 2023; 539:274-277. [PMID: 36574877 DOI: 10.1016/j.cca.2022.12.024] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2022] [Revised: 12/13/2022] [Accepted: 12/22/2022] [Indexed: 12/25/2022]
Abstract
BACKGROUND Next-generation sequencing (NGS) has been suggested as a second-tier diagnostic test for newborn screening, which could help identify the carrier status of hundreds monogenic disorders with wider spectrum and earlier stage. METHODS Among the 1087 children (age from 27 min to 14 years old) underwent liquid chromatography-tandem mass spectrometry (LC-MS/MS), 290 individuals who had at least one abnormal value of LC-MS/MS measurements were sent for amplicon sequencing-based carrier screening (targeting 141 genes for 170 monogenic disorders). Multiplex polymerase chain reaction was used for amplicon capture and library preparation, the NextSeq 500 NGS platform (Illumina PE150) was used for sequencing. The identified clinical significant variants were further validated by Sanger sequencing. RESULTS Only 89 children carry none of clinical significant variants, other 201 individuals carry 1-4 variants in 63 genes (132 types; 317 in total: 171 pathogenic, 37 likely pathogenic, 29 variants of unknown significance, and 80 disease-associated functional polymorphisms). Besides the three missing samples with 4 variants, 91.1 % of identified variants (285 variants in 54 genes) were completely validated by Sanger sequencing. The most common genetic variants were in UGT1A1, GJB2, PAH, G6PD, and SLC25A13 (top 5 genes), which corresponding to Gilbert/Crigler-Najjar symdrome (n = 89), autosomal recessive hearing loss type 1A (n = 58), phenylketonuria (n = 12), glucose-6-phosphate dehydrogenease deficiency (n = 11) and Citrin deficiency (n = 9). More than 42 children present higher phenylalanine in LC-MS/MS, but only 12 of them were identified to carry clinical significant variants in PAH gene. CONCLUSION The amplicon sequencing-based carrier screening in our study could further clarify the abnormal LC-MS/MS results, which could also discover more monogenic disorders uncovered by LC-MS/MS screening.
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Affiliation(s)
- Xu Chen
- Central Laboratory, Baoan Women's and Children's Hospital, Shenzhen, China; Shenzhen Key Laboratory of Birth Defects Research, Shenzhen, China; Institute of Maternal-Fetal Medicine, Baoan Women's and Children's Hospital, Shenzhen, China
| | - Zhongyao Xu
- Shenzhen Uni-medica Technology Co., Ltd, Shenzhen, China
| | - Xianghua Lei
- Shenzhen Uni-medica Technology Co., Ltd, Shenzhen, China
| | - Hui Liang
- Central Laboratory, Baoan Women's and Children's Hospital, Shenzhen, China; Shenzhen Key Laboratory of Birth Defects Research, Shenzhen, China
| | - Feng Wu
- School of Public Health (Shenzhen), Sun Yat-sen University, Shenzhen, China
| | - Ruoqing Chen
- School of Public Health (Shenzhen), Sun Yat-sen University, Shenzhen, China
| | - Yongchao Guo
- Shenzhen Uni-medica Technology Co., Ltd, Shenzhen, China
| | - Likuan Xiong
- Central Laboratory, Baoan Women's and Children's Hospital, Shenzhen, China; Shenzhen Key Laboratory of Birth Defects Research, Shenzhen, China.
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Papiol S, Schulze TG, Heilbronner U. Lithium response in bipolar disorder: Genetics, genomics, and beyond. Neurosci Lett 2022; 785:136786. [PMID: 35817312 DOI: 10.1016/j.neulet.2022.136786] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2022] [Revised: 07/01/2022] [Accepted: 07/06/2022] [Indexed: 11/29/2022]
Abstract
Lithium is an effective mood stabilizer in bipolar disorder (BD). There is, however, high variability in treatment response to lithium and only 20-30% of individuals with BD are excellent responders. This subgroup has been shown to have specific phenotypic characteristics, and family studies have implicated genetics as an important factor. However, candidate gene studies did not find evidence for major effect genes. Genome-wide association studies (GWAS) have emphasized that lithium response is a polygenic trait. GWAS based on larger sample sizes and non-European ancestries are likely to shed light on the genomic architecture of this trait. Furthermore, induced pluripotent stem cells, transcriptomics, epigenetics, the integration of multiple omics data, and their combination with advanced machine learning techniques hold promise for the understanding of the complex biological underpinnings of lithium treatment response.
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Affiliation(s)
- Sergi Papiol
- Institute of Psychiatric Phenomics and Genomics (IPPG), University Hospital, LMU Munich, Munich 80336, Germany; Department of Psychiatry and Psychotherapy, University Hospital, LMU Munich, Munich 80336, Germany.
| | - Thomas G Schulze
- Institute of Psychiatric Phenomics and Genomics (IPPG), University Hospital, LMU Munich, Munich 80336, Germany; Department of Psychiatry and Behavioral Sciences, Johns Hopkins University School of Medicine, Baltimore, MD, USA; Department of Psychiatry and Behavioral Sciences, SUNY Upstate Medical University, Syracuse, NY, USA
| | - Urs Heilbronner
- Institute of Psychiatric Phenomics and Genomics (IPPG), University Hospital, LMU Munich, Munich 80336, Germany
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刘 梦, 张 天. [A review of diagnosis and treatment of syndromic hearing loss]. LIN CHUANG ER BI YAN HOU TOU JING WAI KE ZA ZHI = JOURNAL OF CLINICAL OTORHINOLARYNGOLOGY, HEAD, AND NECK SURGERY 2021; 35:285-288. [PMID: 33794621 PMCID: PMC10128230 DOI: 10.13201/j.issn.2096-7993.2021.03.022] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Subscribe] [Scholar Register] [Received: 02/24/2020] [Indexed: 06/08/2023]
Abstract
Hereditary deafness is divided into syndromic hearing loss and non-syndromic hearing loss according to whether it is accompanied by other system dysfunction. The early identification and diagnosis of syndromic hearing loss is very important, including clinical and molecular diagnosis. Early diagnosis can predict the progress of hearing loss, other systemic disorders and guide treatment. Thus otolaryngologists are likely to become the first doctors to treat children with syndromic hearing loss, it is more necessary to master the clinical and molecular diagnosis methods of common syndromic hearing loss, and cooperate with doctors of other relevant departments for early intervention and treatment. Therefore, this article reviewed the common features, molecular diagnostic methods and treatment strategies for syndromic hearing loss.
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Affiliation(s)
- 梦婷 刘
- 哈尔滨医科大学附属第一医院耳鼻咽喉头颈外科(哈尔滨,150001)
| | - 天虹 张
- 哈尔滨医科大学附属第一医院耳鼻咽喉头颈外科(哈尔滨,150001)
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McInerney-Leo AM, Duncan EL. Massively Parallel Sequencing for Rare Genetic Disorders: Potential and Pitfalls. Front Endocrinol (Lausanne) 2021; 11:628946. [PMID: 33679611 PMCID: PMC7933540 DOI: 10.3389/fendo.2020.628946] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/13/2020] [Accepted: 12/21/2020] [Indexed: 01/04/2023] Open
Abstract
There have been two major eras in the history of gene discovery. The first was the era of linkage analysis, with approximately 1,300 disease-related genes identified by positional cloning by the turn of the millennium. The second era has been powered by two major breakthroughs: the publication of the human genome and the development of massively parallel sequencing (MPS). MPS has greatly accelerated disease gene identification, such that disease genes that would have taken years to map previously can now be determined in a matter of weeks. Additionally, the number of affected families needed to map a causative gene and the size of such families have fallen: de novo mutations, previously intractable by linkage analysis, can be identified through sequencing of the parent-child trio, and genes for recessive disease can be identified through MPS even of a single affected individual. MPS technologies include whole exome sequencing (WES), whole genome sequencing (WGS), and panel sequencing, each with their strengths. While WES has been responsible for most gene discoveries through MPS, WGS is superior in detecting copy number variants, chromosomal rearrangements, and repeat-rich regions. Panels are commonly used for diagnostic purposes as they are extremely cost-effective and generate manageable quantities of data, with no risk of unexpected findings. However, in instances of diagnostic uncertainty, it can be challenging to choose the right panel, and in these circumstances WES has a higher diagnostic yield. MPS has ethical, social, and legal implications, many of which are common to genetic testing generally but amplified due to the magnitude of data (e.g., relationship misattribution, identification of variants of uncertain significance, and genetic discrimination); others are unique to WES and WGS technologies (e.g., incidental or secondary findings). Nonetheless, MPS is rapidly translating into clinical practice as an extremely useful part of the clinical armamentarium.
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Affiliation(s)
- Aideen M. McInerney-Leo
- Dermatology Research Centre, University of Queensland Diamantina Institute, The University of Queensland, Brisbane, QLD, Australia
| | - Emma L. Duncan
- Department of Twin Research & Genetic Epidemiology, Faculty of Life Sciences and Medicine, School of Life Course Sciences, King’s College London, London, United Kingdom
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Liu Y, Zhao XD. A Three-Generation Pedigree of Multifocal Heterotopic Ossification With Bilateral Involvement. Orthopedics 2021; 44:e139-e145. [PMID: 33089331 DOI: 10.3928/01477447-20201007-01] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/29/2019] [Accepted: 01/20/2020] [Indexed: 02/03/2023]
Abstract
Heterotopic ossification (HO) can be classified as nonhereditary HO (NHHO) or hereditary HO (HHO). Hereditary HO includes 2 different forms: fibrodysplasia ossificans progressiva (FOP) and progressive osseous heteroplasia (POH). Each of these disorders is caused by mutations in a single (different) gene. Clinical diagnosis of FOP can be confirmed by sequence analysis of the ACVR1 gene. Fewer than 10 families with autosomal dominant inheritance of FOP have been reported. The authors report clinical manifestations, pedigree analysis, and mutational analysis of the ACVR1 in a 3-generation Chinese family with 4 individuals presenting multifocal and bilateral involvement of HO. Clinical features of affected individuals of the family were not consistent with the classic FOP or atypical FOP. Exon sequencing was performed on every family member and 3 sporadic NHHO patients who did not belong to this family. All family members and 3 sporadic NHHO patients carried 2 hereditary homozygous silent mutations- c.270C>T and c.690G>A-the new and unique mutations in ACVR1. These results may suggest that the affected individuals in this family present a novel FOP-variant syndrome or a new form of HHO. To the authors' knowledge, this is the first well-documented instance of a 3-generation Chinese family with multifocal and bilateral involvement of HO. [Orthopedics. 2021;44(1):e139-e145.].
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Fisher L, Fisher A, Smith PN. Helicobacter pylori Related Diseases and Osteoporotic Fractures (Narrative Review). J Clin Med 2020; 9:E3253. [PMID: 33053671 PMCID: PMC7600664 DOI: 10.3390/jcm9103253] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2020] [Revised: 09/28/2020] [Accepted: 10/07/2020] [Indexed: 02/06/2023] Open
Abstract
Osteoporosis (OP) and osteoporotic fractures (OFs) are common multifactorial and heterogenic disorders of increasing incidence. Helicobacter pylori (H.p.) colonizes the stomach approximately in half of the world's population, causes gastroduodenal diseases and is prevalent in numerous extra-digestive diseases known to be associated with OP/OF. The studies regarding relationship between H.p. infection (HPI) and OP/OFs are inconsistent. The current review summarizes the relevant literature on the potential role of HPI in OP, falls and OFs and highlights the reasons for controversies in the publications. In the first section, after a brief overview of HPI biological features, we analyze the studies evaluating the association of HPI and bone status. The second part includes data on the prevalence of OP/OFs in HPI-induced gastroduodenal diseases (peptic ulcer, chronic/atrophic gastritis and cancer) and the effects of acid-suppressive drugs. In the next section, we discuss the possible contribution of HPI-associated extra-digestive diseases and medications to OP/OF, focusing on conditions affecting both bone homeostasis and predisposing to falls. In the last section, we describe clinical implications of accumulated data on HPI as a co-factor of OP/OF and present a feasible five-step algorithm for OP/OF risk assessment and management in regard to HPI, emphasizing the importance of an integrative (but differentiated) holistic approach. Increased awareness about the consequences of HPI linked to OP/OF can aid early detection and management. Further research on the HPI-OP/OF relationship is needed to close current knowledge gaps and improve clinical management of both OP/OF and HPI-related disorders.
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Affiliation(s)
- Leon Fisher
- Department of Gastroenterology, Frankston Hospital, Peninsula Health, Melbourne 3199, Australia
| | - Alexander Fisher
- Department of Geriatric Medicine, The Canberra Hospital, ACT Health, Canberra 2605, Australia;
- Department of Orthopedic Surgery, The Canberra Hospital, ACT Health, Canberra 2605, Australia;
- Australian National University Medical School, Canberra 2605, Australia
| | - Paul N Smith
- Department of Orthopedic Surgery, The Canberra Hospital, ACT Health, Canberra 2605, Australia;
- Australian National University Medical School, Canberra 2605, Australia
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Cabrera AP, Monickaraj F, Rangasamy S, Hobbs S, McGuire P, Das A. Do Genomic Factors Play a Role in Diabetic Retinopathy? J Clin Med 2020; 9:jcm9010216. [PMID: 31947513 PMCID: PMC7019561 DOI: 10.3390/jcm9010216] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2019] [Revised: 01/06/2020] [Accepted: 01/09/2020] [Indexed: 02/07/2023] Open
Abstract
Although there is strong clinical evidence that the control of blood glucose, blood pressure, and lipid level can prevent and slow down the progression of diabetic retinopathy (DR) as shown by landmark clinical trials, it has been shown that these factors only account for 10% of the risk for developing this disease. This suggests that other factors, such as genetics, may play a role in the development and progression of DR. Clinical evidence shows that some diabetics, despite the long duration of their diabetes (25 years or more) do not show any sign of DR or show minimal non-proliferative diabetic retinopathy (NPDR). Similarly, not all diabetics develop proliferative diabetic retinopathy (PDR). So far, linkage analysis, candidate gene studies, and genome-wide association studies (GWAS) have not produced any statistically significant results. We recently initiated a genomics study, the Diabetic Retinopathy Genetics (DRGen) Study, to examine the contribution of rare and common variants in the development of different phenotypes of DR, as well as their responsiveness to anti-VEGF treatment in diabetic macular edema (DME). Our preliminary findings reveal a novel set of genetic variants involved in the angiogenesis and inflammatory pathways that contribute to DR progression or protection. Further investigation of variants can help to develop novel biomarkers and lead to new therapeutic targets in DR.
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Affiliation(s)
- Andrea P. Cabrera
- Department of Surgery/Ophthalmology, University of New Mexico School of Medicine, Albuquerque, NM 87131, USA; (A.P.C.); (F.M.); (S.H.)
| | - Finny Monickaraj
- Department of Surgery/Ophthalmology, University of New Mexico School of Medicine, Albuquerque, NM 87131, USA; (A.P.C.); (F.M.); (S.H.)
- New Mexico VA Health Care System, Albuquerque, NM 87131, USA
| | | | - Sam Hobbs
- Department of Surgery/Ophthalmology, University of New Mexico School of Medicine, Albuquerque, NM 87131, USA; (A.P.C.); (F.M.); (S.H.)
| | - Paul McGuire
- Department of Cell Biology & Physiology, UNM, Albuquerque, NM 87131, USA;
| | - Arup Das
- Department of Surgery/Ophthalmology, University of New Mexico School of Medicine, Albuquerque, NM 87131, USA; (A.P.C.); (F.M.); (S.H.)
- New Mexico VA Health Care System, Albuquerque, NM 87131, USA
- Department of Cell Biology & Physiology, UNM, Albuquerque, NM 87131, USA;
- Correspondance:
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8
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Zeeshan S, Xiong R, Liang BT, Ahmed Z. 100 Years of evolving gene-disease complexities and scientific debutants. Brief Bioinform 2019; 21:885-905. [PMID: 30972412 DOI: 10.1093/bib/bbz038] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2019] [Revised: 03/06/2019] [Accepted: 03/08/2019] [Indexed: 12/22/2022] Open
Abstract
It's been over 100 years since the word `gene' is around and progressively evolving in several scientific directions. Time-to-time technological advancements have heavily revolutionized the field of genomics, especially when it's about, e.g. triple code development, gene number proposition, genetic mapping, data banks, gene-disease maps, catalogs of human genes and genetic disorders, CRISPR/Cas9, big data and next generation sequencing, etc. In this manuscript, we present the progress of genomics from pea plant genetics to the human genome project and highlight the molecular, technical and computational developments. Studying genome and epigenome led to the fundamentals of development and progression of human diseases, which includes chromosomal, monogenic, multifactorial and mitochondrial diseases. World Health Organization has classified, standardized and maintained all human diseases, when many academic and commercial online systems are sharing information about genes and linking to associated diseases. To efficiently fathom the wealth of this biological data, there is a crucial need to generate appropriate gene annotation repositories and resources. Our focus has been how many gene-disease databases are available worldwide and which sources are authentic, timely updated and recommended for research and clinical purposes. In this manuscript, we have discussed and compared 43 such databases and bioinformatics applications, which enable users to connect, explore and, if possible, download gene-disease data.
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Affiliation(s)
- Saman Zeeshan
- The Jackson Laboratory for Genomic Medicine, 10 Discovery Drive, Farmington, CT, USA
| | - Ruoyun Xiong
- Department of Genetics and Genome Sciences, School of Medicine, University of Connecticut Health Center, Farmington Ave, Farmington, CT, USA
| | - Bruce T Liang
- Department of Genetics and Genome Sciences, School of Medicine, University of Connecticut Health Center, Farmington Ave, Farmington, CT, USA.,Pat and Jim Calhoun Cardiology Center, School of Medicine, University of Connecticut Health Center, Farmington Ave, Farmington, CT, USA
| | - Zeeshan Ahmed
- Department of Genetics and Genome Sciences, School of Medicine, University of Connecticut Health Center, Farmington Ave, Farmington, CT, USA
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Kaur Y, de Souza RJ, Gibson WT, Meyre D. A systematic review of genetic syndromes with obesity. Obes Rev 2017; 18:603-634. [PMID: 28346723 DOI: 10.1111/obr.12531] [Citation(s) in RCA: 104] [Impact Index Per Article: 14.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/09/2016] [Revised: 02/01/2017] [Accepted: 02/02/2017] [Indexed: 11/29/2022]
Abstract
Syndromic monogenic obesity typically follows Mendelian patterns of inheritance and involves the co-presentation of other characteristics, such as mental retardation, dysmorphic features and organ-specific abnormalities. Previous reviews on obesity have reported 20 to 30 syndromes but no systematic review has yet been conducted on syndromic obesity. We searched seven databases using terms such as 'obesity', 'syndrome' and 'gene' to conduct a systematic review of literature on syndromic obesity. Our literature search identified 13,719 references. After abstract and full-text review, 119 relevant papers were eligible, and 42 papers were identified through additional searches. Our analysis of these 161 papers found that 79 obesity syndromes have been reported in literature. Of the 79 syndromes, 19 have been fully genetically elucidated, 11 have been partially elucidated, 27 have been mapped to a chromosomal region and for the remaining 22, neither the gene(s) nor the chromosomal location(s) have yet been identified. Interestingly, 54.4% of the syndromes have not been assigned a name, whereas 13.9% have more than one name. We report on organizational inconsistencies (e.g. naming discrepancies and syndrome classification) and provide suggestions for improvements. Overall, this review illustrates the need for increased clinical and genetic research on syndromes with obesity.
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Affiliation(s)
- Y Kaur
- Department of Health Research Methods, Evidence, and Impact, McMaster University, Hamilton, Canada
| | - R J de Souza
- Department of Health Research Methods, Evidence, and Impact, McMaster University, Hamilton, Canada
| | - W T Gibson
- Department of Medical Genetics, University of British Columbia, Vancouver, Canada.,British Columbia Children's Hospital Research Institute, Vancouver, Canada
| | - D Meyre
- Department of Health Research Methods, Evidence, and Impact, McMaster University, Hamilton, Canada.,Department of Pathology and Molecular Medicine, McMaster University, Hamilton, Canada
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Kaput J, Perozzi G, Radonjic M, Virgili F. Propelling the paradigm shift from reductionism to systems nutrition. GENES & NUTRITION 2017; 12:3. [PMID: 28138347 PMCID: PMC5264346 DOI: 10.1186/s12263-016-0549-8] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 12/08/2016] [Accepted: 12/13/2016] [Indexed: 12/14/2022]
Abstract
The complex physiology of living organisms represents a challenge for mechanistic understanding of the action of dietary bioactives in the human body and of their possible role in health and disease. Animal, cell, and microbial models have been extensively used to address questions that could not be pursued experimentally in humans, posing an additional level of complexity in translation of the results to healthy and diseased metabolism. The past few decades have witnessed a surge in development of increasingly sensitive molecular techniques and bioinformatic tools for storing, managing, and analyzing increasingly large datasets. Application of such powerful means to molecular nutrition research led to a major leap in study designs and experimental approaches yielding experimental data connecting dietary components to human health. Scientific journals bear major responsibilities in the advancement of science. As primary actors of dissemination to the scientific community, journals can impose rigid criteria for publishing only sound, reliable, and reproducible data. Journal policies are meant to guide potential authors to adopt the most updated standardization guidelines and shared best practices. Such policies evolve in parallel with the evolution of novel approaches and emerging challenges and therefore require constant updating. We highlight in this manuscript the major scientific issues that led to formulating new, updated journal policies for Genes & Nutrition, a journal which targets the growing field of nutritional systems biology interfacing personalized nutrition and preventive medicine, with the ultimate goal of promoting health and preventing or treating disease. We focus here on relevant issues requiring standardization in nutrition research. We also introduce new sections on human genetic variation and nutritional bioinformatics which follow the evolution of nutritional science into the twenty-first century.
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Affiliation(s)
- Jim Kaput
- Nestle Institute of Health Sciences, Lausanne, Switzerland
| | | | | | - Fabio Virgili
- CREA-NUT, Food & Nutrition Research Centre, Rome, Italy
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Al-Attas A, Assidi M, Al-Maghrabi J, Dallol A, Schulten HJ, Abu-Elmagd M, Chaudhary A, Abuzenadah A, Budowle B, Buhmeida A, Al-Qahtani M. Enhancement of Pathologist's Routine Practice: Reuse of DNA Extracted from Immunostained Formalin-fixed Paraffin-embedded (FFPE) Slides in Downstream Molecular Analysis of Cancer. Cancer Genomics Proteomics 2016; 13:399-406. [PMID: 27566658 PMCID: PMC5070629] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2016] [Accepted: 06/13/2016] [Indexed: 06/06/2023] Open
Abstract
BACKGROUND/AIM To date, the conventional formalin-fixed, paraffin-embedded (FFPE) technique is the gold-standard for preserving histomorphology. Once FFPE tissues are stained, slides are routinely archived along with their blocks at biobanks/hospitals. However, the reuse of fixed and stained biospecimens as DNA source is not a common routine practice worldwide and, thus, indicates the need of studies to investigate the feasibility of extracting DNA from already immunohistochemistry (IHC) FFPE-stained slides and its possible reuse in subsequent downstream molecular analyses. MATERIALS AND METHODS FFPE IHC slides from colorectal cancer (CRC) patients were prepared and stored in the CEGMR Biobank. The workflow consists of digitalization of IHC stained slide's image, removing the slide cover-slip, crude dissection and DNA extraction. Following DNA quality assessment, mutation analysis of CTNNB1 and methylation profile of CDH1 were performed. RESULTS High-quality DNA was obtained allowing 60% concordance between CDH1 methylation and membranous E-cadherin expression pattern. Clean CTNNB1 DNA chromatograms with evenly-spaced peaks were observed. CONCLUSION This study is a proof of concept to recycle and reuse DNA from IHC stained slides with suitable concentration and integrity for further downstream molecular applications. These findings will enhance the pathologists' knowledge, attitudes and practices (KAP) towards the use of these biospecimens and support the implementation of this approach in clinical pathology practice. Therefore, the scientific community will benefit from the largest comprehensive database of human fully annotated FFPE biospecimens already available at their disposal in order to demystify the complexity and the heterogeneity of many challenging diseases and foster the transition towards precision medicine.
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Affiliation(s)
- Asmaa Al-Attas
- Center of Excellence in Genomic Medicine Research, King Abdulaziz University, Jeddah, Kingdom of Saudi Arabia
| | - Mourad Assidi
- Center of Excellence in Genomic Medicine Research, King Abdulaziz University, Jeddah, Kingdom of Saudi Arabia KACST Technology Innovation Center in Personalized Medicine, King Abdulaziz University, Jeddah, Kingdom of Saudi Arabia
| | - Jaudah Al-Maghrabi
- Department of Pathology, Faculty of Medicine, King Abdulaziz University, Jeddah, Kingdom of Saudi Arabia
| | - Ashraf Dallol
- Center of Excellence in Genomic Medicine Research, King Abdulaziz University, Jeddah, Kingdom of Saudi Arabia KACST Technology Innovation Center in Personalized Medicine, King Abdulaziz University, Jeddah, Kingdom of Saudi Arabia
| | - Hans-Juergen Schulten
- Center of Excellence in Genomic Medicine Research, King Abdulaziz University, Jeddah, Kingdom of Saudi Arabia
| | - Muhammad Abu-Elmagd
- Center of Excellence in Genomic Medicine Research, King Abdulaziz University, Jeddah, Kingdom of Saudi Arabia
| | - Adeel Chaudhary
- Center of Excellence in Genomic Medicine Research, King Abdulaziz University, Jeddah, Kingdom of Saudi Arabia
| | - Adel Abuzenadah
- Center of Excellence in Genomic Medicine Research, King Abdulaziz University, Jeddah, Kingdom of Saudi Arabia KACST Technology Innovation Center in Personalized Medicine, King Abdulaziz University, Jeddah, Kingdom of Saudi Arabia
| | - Bruce Budowle
- Center of Excellence in Genomic Medicine Research, King Abdulaziz University, Jeddah, Kingdom of Saudi Arabia Institute of Applied Genetics, Department of Molecular and Medical Genetics, University of North Texas Health Science Center, Fort Worth, TX, U.S.A
| | - Abdelbaset Buhmeida
- Center of Excellence in Genomic Medicine Research, King Abdulaziz University, Jeddah, Kingdom of Saudi Arabia
| | - Mohammed Al-Qahtani
- Center of Excellence in Genomic Medicine Research, King Abdulaziz University, Jeddah, Kingdom of Saudi Arabia
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Mostovoy Y, Levy-Sakin M, Lam J, Lam ET, Hastie AR, Marks P, Lee J, Chu C, Lin C, Džakula Ž, Cao H, Schlebusch SA, Giorda K, Schnall-Levin M, Wall JD, Kwok PY. A hybrid approach for de novo human genome sequence assembly and phasing. Nat Methods 2016; 13:587-90. [PMID: 27159086 PMCID: PMC4927370 DOI: 10.1038/nmeth.3865] [Citation(s) in RCA: 151] [Impact Index Per Article: 18.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2016] [Accepted: 04/08/2016] [Indexed: 12/11/2022]
Abstract
Despite tremendous progress in genome sequencing, the basic goal of producing phased (haplotype-resolved) genome sequence with end-to-end contiguity for each chromosome at reasonable cost and effort is still unrealized. In this study, we describe a new approach to perform de novo genome assembly and experimental phasing by integrating the data from Illumina short-read sequencing, 10X Genomics Linked-Read sequencing, and BioNano Genomics genome mapping to yield a high-quality, phased, de novo assembled human genome.
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Affiliation(s)
- Yulia Mostovoy
- Cardiovascular Research Institute, University of California, San Francisco, San Francisco, California, USA
| | - Michal Levy-Sakin
- Cardiovascular Research Institute, University of California, San Francisco, San Francisco, California, USA
| | - Jessica Lam
- Cardiovascular Research Institute, University of California, San Francisco, San Francisco, California, USA
| | - Ernest T Lam
- BioNano Genomics, Inc., San Diego, California, USA
| | | | | | - Joyce Lee
- BioNano Genomics, Inc., San Diego, California, USA
| | - Catherine Chu
- Cardiovascular Research Institute, University of California, San Francisco, San Francisco, California, USA
| | - Chin Lin
- Cardiovascular Research Institute, University of California, San Francisco, San Francisco, California, USA
| | | | - Han Cao
- BioNano Genomics, Inc., San Diego, California, USA
| | - Stephen A Schlebusch
- Department of Molecular and Cell Biology, University of Cape Town, Cape Town, South Africa
| | | | | | - Jeffrey D Wall
- Institute for Human Genetics, University of California, San Francisco, San Francisco, California, USA
| | - Pui-Yan Kwok
- Cardiovascular Research Institute, University of California, San Francisco, San Francisco, California, USA.,Institute for Human Genetics, University of California, San Francisco, San Francisco, California, USA.,Department of Dermatology, University of California, San Francisco, San Francisco, California, USA
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13
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Rivadeneira F, Mäkitie O. Osteoporosis and Bone Mass Disorders: From Gene Pathways to Treatments. Trends Endocrinol Metab 2016; 27:262-281. [PMID: 27079517 DOI: 10.1016/j.tem.2016.03.006] [Citation(s) in RCA: 82] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/12/2016] [Revised: 03/04/2016] [Accepted: 03/06/2016] [Indexed: 12/28/2022]
Abstract
Genomic technologies have evolved rapidly contributing to the understanding of diseases. Genome-wide association studies (GWAS) and whole-exome sequencing have aided the identification of the genetic determinants of monogenic and complex conditions including osteoporosis and bone mass disorders. Overlap exists between the genes implicated in monogenic and complex forms of bone mass disorders, largely explained by the clustering of genes encoding factors in signaling pathways crucial for mesenchymal cell differentiation, skeletal development, and bone remodeling and metabolism. Numerous of the remaining discovered genes merit functional follow-up studies to elucidate their role in bone biology. The insight provided by genetic studies is serving the identification of biomarkers predictive of disease, redefining disease, response to treatment, and discovery of novel drug targets for skeletal disorders.
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Affiliation(s)
- Fernando Rivadeneira
- Musculoskeletal Genomics, Health and Metabolism, Departments of Internal Medicine and Epidemiology, Erasmus University Medical Center, 3000CA Rotterdam, The Netherlands.
| | - Outi Mäkitie
- Children's Hospital, University of Helsinki and Helsinki University Hospital, Helsinki, Finland; Department of Molecular Medicine and Surgery, Karolinska Institutet, and Clinical Genetics, Karolinska University Hospital, 171 76 Stockholm, Sweden
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14
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Steffen P, Kwiatkowski M, Robertson WD, Zarrine-Afsar A, Deterra D, Richter V, Schlüter H. Protein species as diagnostic markers. J Proteomics 2016; 134:5-18. [DOI: 10.1016/j.jprot.2015.12.015] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2015] [Revised: 11/28/2015] [Accepted: 12/09/2015] [Indexed: 02/07/2023]
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15
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Qin Y, Gao WQ. Concise Review: Patient-Derived Stem Cell Research for Monogenic Disorders. Stem Cells 2015; 34:44-54. [DOI: 10.1002/stem.2112] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2015] [Revised: 06/05/2015] [Accepted: 06/20/2015] [Indexed: 12/24/2022]
Affiliation(s)
- Yiren Qin
- State Key Laboratory of Oncogenes and Related Genes, Renji-Med-X Clinical Stem Cell Research Center, Ren Ji Hospital, School of Medicine; hanghai Jiao Tong University; Shanghai People's Republic of China
| | - Wei-Qiang Gao
- State Key Laboratory of Oncogenes and Related Genes, Renji-Med-X Clinical Stem Cell Research Center, Ren Ji Hospital, School of Medicine; hanghai Jiao Tong University; Shanghai People's Republic of China
- School of Biomedical Engineering & Med-X Research Institute; Shanghai Jiao Tong University; Shanghai People's Republic of China
- Collaborative Innovation Center of Systems Biomedicine; Shanghai Jiao Tong University; Shanghai People's Republic of China
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16
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Lächelt U, Wagner E. Nucleic Acid Therapeutics Using Polyplexes: A Journey of 50 Years (and Beyond). Chem Rev 2015; 115:11043-78. [DOI: 10.1021/cr5006793] [Citation(s) in RCA: 418] [Impact Index Per Article: 46.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Affiliation(s)
- Ulrich Lächelt
- Pharmaceutical
Biotechnology, Department of Pharmacy, Ludwig Maximilians Universität, 81377 Munich, Germany
- Nanosystems
Initiative
Munich (NIM), 80799 Munich, Germany
| | - Ernst Wagner
- Pharmaceutical
Biotechnology, Department of Pharmacy, Ludwig Maximilians Universität, 81377 Munich, Germany
- Nanosystems
Initiative
Munich (NIM), 80799 Munich, Germany
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