Detection of Chromosomal Aberrations in Clinical Practice: From Karyotype to Genome Sequence.

Annu Rev Genomics Hum Genet. 2015;16:309-26

Authors: Martin CL, Warburton D

Abstract
Since the inception of clinical cytogenetics in the late 1950s, the field has witnessed the evolution of multiple methodologies for the evaluation of chromosomal imbalances and rearrangements. From the replacement of solidly stained chromosomes by Giemsa banding (G-banding) to in situ hybridization and microarrays, each technique has sought to detect smaller and smaller chromosomal aberrations across the genome. Microarray analysis has revealed that copy-number variants-a class of mutation resulting from the loss (deletion) or gain (duplication) of genomic material that is >1 kb in size-are among the significant contributors to human disease and normal variation. Here, we evaluate the history and utility of various methodologies and their impact on the current practice of clinical cytogenetics.

PMID: 26077817 [PubMed - indexed for MEDLINE]

Genome-wide microarray analysis of gene expression profiling in major depression and antidepressant therapy.

Prog Neuropsychopharmacol Biol Psychiatry. 2016 Jan 4;64:334-40

Authors: Lin E, Tsai SJ

Abstract
Major depressive disorder (MDD) is a serious health concern worldwide. Currently there are no predictive tests for the effectiveness of any particular antidepressant in an individual patient. Thus, doctors must prescribe antidepressants based on educated guesses. With the recent advent of scientific research, genome-wide gene expression microarray studies are widely utilized to analyze hundreds of thousands of biomarkers by high-throughput technologies. In addition to the candidate-gene approach, the genome-wide approach has recently been employed to investigate the determinants of MDD as well as antidepressant response to therapy. In this review, we mainly focused on gene expression studies with genome-wide approaches using RNA derived from peripheral blood cells. Furthermore, we reviewed their limitations and future directions with respect to the genome-wide gene expression profiling in MDD pathogenesis as well as in antidepressant therapy.

PMID: 25708651 [PubMed - indexed for MEDLINE]

Fluorescence-based bioassays for the detection and evaluation of food materials.

Sensors (Basel). 2015;15(10):25831-67

Authors: Nishi K, Isobe S, Zhu Y, Kiyama R

Abstract
We summarize here the recent progress in fluorescence-based bioassays for the detection and evaluation of food materials by focusing on fluorescent dyes used in bioassays and applications of these assays for food safety, quality and efficacy. Fluorescent dyes have been used in various bioassays, such as biosensing, cell assay, energy transfer-based assay, probing, protein/immunological assay and microarray/biochip assay. Among the arrays used in microarray/biochip assay, fluorescence-based microarrays/biochips, such as antibody/protein microarrays, bead/suspension arrays, capillary/sensor arrays, DNA microarrays/polymerase chain reaction (PCR)-based arrays, glycan/lectin arrays, immunoassay/enzyme-linked immunosorbent assay (ELISA)-based arrays, microfluidic chips and tissue arrays, have been developed and used for the assessment of allergy/poisoning/toxicity, contamination and efficacy/mechanism, and quality control/safety. DNA microarray assays have been used widely for food safety and quality as well as searches for active components. DNA microarray-based gene expression profiling may be useful for such purposes due to its advantages in the evaluation of pathway-based intracellular signaling in response to food materials.

PMID: 26473869 [PubMed - indexed for MEDLINE]

Recent developments in multiplexing techniques for immunohistochemistry.

Expert Rev Mol Diagn. 2015;15(9):1171-86

Authors: Dixon AR, Bathany C, Tsuei M, White J, Barald KF, Takayama S

Abstract
Methods to detect immunolabeled molecules at increasingly higher resolutions, even when present at low levels, are revolutionizing immunohistochemistry (IHC). These technologies can be valuable for the management and examination of rare patient tissue specimens, and for improved accuracy of early disease detection. The purpose of this article is to highlight recent multiplexing methods that are candidates for more prevalent use in clinical research and potential translation to the clinic. Multiplex IHC methods, which permit identification of at least 3 and up to 30 discrete antigens, have been divided into whole-section staining and spatially-patterned staining categories. Associated signal enhancement technologies that can enhance performance and throughput of multiplex IHC assays are also discussed. Each multiplex IHC technique, detailed herein, is associated with several advantages as well as tradeoffs that must be taken into consideration for proper evaluation and use of the methods.

PMID: 26289603 [PubMed - indexed for MEDLINE]

[Identification of proteomic biomarkers of preeclampsia using protein microarray and tandem mass spectrometry].

Postepy Hig Med Dosw (Online). 2015;69:562-70

Authors: Charkiewicz K, Jasinska E, Laudanski P

Abstract
Preeclampsia (PE) is the leading cause of death of the fetus and the mother. The exact pathomechanism has not so far been clarified. PE coexists with many other diseases, but it is often difficult to explain the association between them and find a clear reason for their occurrence. There are many predictive factors, but none are highly specific in preeclampsia. The diagnosis of preeclampsia seems to be very complex, which is another argument for the exploration of knowledge on this subject. Although many of the discoveries have hitherto been made in the field of proteomics, still no single specific biomarker of preeclampsia has been discovered. Research at the genome level is important because it can help us understand the genetic predisposition of patients affected by this disease. Nevertheless, researchers have recently become more interested in the pathophysiology of PE, and they are trying to answer the question: what is the real, direct cause of preeclampsia? Thus, the discovery of a protein that is a good predictor of preeclampsia development would significantly accelerate the medical care of pregnant women, and consequently reduce the risk of occurrence of HELLP syndrome and fetal death. Apart from the predictive and diagnostic function, such a discovery would help us to better understand the pathogenesis of preeclampsia and to find in the future a medical drug to suppress this disease. In order to make a breakthrough in this field, scientists need to use the most modern methods of proteomics, which allow for the analysis of small amounts of biological material in the shortest possible time, thereby giving a lot of information about existing proteins in the sample. Such optimization allows two methods, most commonly used by researchers: tandem mass spectrometry and protein microarray technique.

PMID: 25983295 [PubMed - indexed for MEDLINE]

[Functional annotation of rice WRKY transcription factors based on their transcriptional features].

Yi Chuan. 2016 Feb;38(2):126-36

Authors: Liyun L, Jianan S, Shuo Y, Caiqiang S, Guozhen L

Abstract
Transcription factors regulate alteration of transcription levels. Recently, huge amount of transcriptomic data are accumulated via the application of high throughput sequencing technology, and it is reasonable to postulate that in-depth analysis of transcription data could be used to enhance gene annotation. In this study, we chose the gene family of rice WRKY transcription factors. Based on literature search, the transcriptional data under different biological processes, including biotic and abiotic stress, development, and nutrient absorption and hormone treatments were analyzed systematically. To the end, we summarize the list of differentially expressed WRKY genes. We also expect that such information will enrich their functional annotation and also provide direct clues for subsequent functional studies.

PMID: 26907776 [PubMed - indexed for MEDLINE]

Autoantigen Microarray for High-throughput Autoantibody Profiling in Systemic Lupus Erythematosus.

Genomics Proteomics Bioinformatics. 2015 Aug;13(4):210-8

Authors: Zhu H, Luo H, Yan M, Zuo X, Li QZ

Abstract
Systemic lupus erythematosus (SLE) is a complex autoimmune disease characterized by the production of autoantibodies to a broad range of self-antigens. Profiling the autoantibody repertoire using array-based technology has emerged as a powerful tool for the identification of biomarkers in SLE and other autoimmune diseases. Proteomic microarray has the capacity to hold large number of self-antigens on a solid surface and serve as a high-throughput screening method for the determination of autoantibody specificities. The autoantigen arrays carrying a wide variety of self-antigens, such as cell nuclear components (nucleic acids and associated proteins), cytoplasmic proteins, phospholipid proteins, cell matrix proteins, mucosal/secreted proteins, glomeruli, and other tissue-specific proteins, have been used for screening of autoantibody specificities associated with different manifestations of SLE. Arrays containing synthetic peptides and molecular modified proteins are also being utilized for identification of autoantibodies targeting to special antigenic epitopes. Different isotypes of autoantibodies, including IgG, IgM, IgA, and IgE, as well as other Ig subtypes, can be detected simultaneously with multi-color labeled secondary antibodies. Serum and plasma are the most common biologic materials for autoantibody detection, but other body fluids such as cerebrospinal fluid, synovial fluid, and saliva can also be a source of autoantibody detection. Proteomic microarray as a multiplexed high-throughput screening platform is playing an increasingly-important role in autoantibody diagnostics. In this article, we highlight the use of autoantigen microarrays for autoantibody exploration in SLE.

PMID: 26415621 [PubMed - indexed for MEDLINE]

Molecular cytopathology for thyroid nodules: A review of methodology and test performance.

Cancer Cytopathol. 2016 Jan;124(1):14-27

Authors: Nishino M

Abstract
Advances in the molecular characterization of thyroid cancers have fueled the development of genetic and gene expression-based tests for thyroid fine-needle aspirations. Collectively, these tests are designed to improve the diagnostic certainty of thyroid cytology. This review summarizes the early published experience with the commercially available versions of these tests: the Afirma Gene Expression Classifier, ThyGenX (formerly miRInform)/ThyraMIR, and ThyroSeq. Key differences in testing approaches and issues regarding test performance and interpretation are also discussed.

PMID: 26348024 [PubMed - indexed for MEDLINE]

RNA-Seq: Improving Our Understanding of Retinal Biology and Disease.

Cold Spring Harb Perspect Med. 2015;5(9):a017152

Authors: Farkas MH, Au ED, Sousa ME, Pierce EA

Abstract
Over the past several years, rapid technological advances have allowed for a dramatic increase in our knowledge and understanding of the transcriptional landscape, because of the ability to study gene expression in greater depth and with more detail than previously possible. To this end, RNA-Seq has quickly become one of the most widely used methods for studying transcriptomes of tissues and individual cells. Unlike previously favored analysis methods, RNA-Seq is extremely high-throughput, and is not dependent on an annotated transcriptome, laying the foundation for novel genetic discovery. Additionally, RNA-Seq derived transcriptomes provide a basis for widening the scope of research to identify potential targets in the treatment of retinal disease.

PMID: 25722474 [PubMed - indexed for MEDLINE]

Recent advances and future applications of microfluidic live-cell microarrays.

Biotechnol Adv. 2015 Nov 1;33(6 Pt 1):948-61

Authors: Rothbauer M, Wartmann D, Charwat V, Ertl P

Abstract
Microfluidic live-cell microarrays show much promise as screening tools for biomedical research because they could shed light on key biological processes such as cell signaling and cell-to-cell and cell-to-substrate dynamic responses. While miniaturization reduces the need for expensive clinical grade reagents, the integration of functional components including micropumps, biosensors, actuators, mixers and gradient generators results in improved assay reliability, reproducibility and well-defined cell culture conditions. The present review addresses recent technological advances in microfluidic live-cell microarray technology with a special focus on the applications of microfluidic single-cell, multi-cell and 3D cell microarrays.

PMID: 26133396 [PubMed - indexed for MEDLINE]

The Contribution of Transcriptomics to Biomarker Development in Systemic Vasculitis and SLE.

Curr Pharm Des. 2015;21(17):2225-35

Authors: Flint SM, McKinney EF, Lyons PA, Smith KG

Abstract
A small but increasing number of gene expression based biomarkers are becoming available for routine clinical use, principally in oncology and transplantation. These underscore the potential of gene expression arrays and RNA sequencing for biomarker development, but this potential has not yet been fully realized and most candidates do not progress beyond the initial report. The first part of this review examines the process of gene expression- based biomarker development, highlighting how systematic biases and confounding can significantly skew study outcomes. Adequate validation in an independent cohort remains the single best means of protecting against these concerns. The second part considers gene-expression based biomarkers in Systemic Lupus Erythematosus (SLE) and systemic vasculitis. The type 1 interferon inducible gene signature remains by far the most studied in autoimmune rheumatic disease. While initially presented as an objective, blood-based biomarker of active SLE, subsequent research has shown that it is not specific to SLE and that its association with disease activity is considerably more nuanced than first thought. Nonetheless, it is currently under evaluation in ongoing trials of anti-interferon therapy. Other candidate markers of note include a prognostic CD8+ T-cell gene signature validated in SLE and ANCA-associated vasculitis, and a disease activity biomarker for SLE derived from modules of tightly correlated genes.

PMID: 25771200 [PubMed - indexed for MEDLINE]

2025 Jan 15. Drugs and Lactation Database (LactMed®) [Internet]. Bethesda (MD): National Institute of Child Health and Human Development; 2006–.

ABSTRACT

No information is available on milk or infant serum levels of vanzacaftor or deutivacaftor. Information from mother-infant pairs with elexacaftor, ivacaftor and tezacaftor indicates that tezacaftor has low levels in milk and infant serum. Deutivacaftor is a deuterated form of ivacaftor that has slower clearance, a longer half-life and greater maternal exposure. Transient mild elevations in bilirubin and liver enzymes during maternal therapy have been reported in breastfed infants whose mothers were taking another combination product containing tezacaftor and ivacaftor. Enzyme levels tended to normalize during continued breastfeeding. Until more data are available, monitoring of infant bilirubin and liver enzymes might be advisable during breastfeeding with maternal vanzacaftor, tezacaftor and deutivacaftor therapy.[1] Congenital cataracts in breastfed infants has been reported in the infants of mothers who took drugs of this class during pregnancy. Examination of breastfed infants for cataracts has been recommended.[2] Anecdotal evidence indicates that these types of drugs in breastmilk may moderate cystic fibrosis in breastfed infants.

PMID:39836862 | Bookshelf:NBK611184

2021 Apr 19. Drugs and Lactation Database (LactMed) [Internet]. Bethesda (MD): National Library of Medicine (US); 2006–.

ABSTRACT

Information from one maternal-infant pair with ivacaftor and lumacaftor indicates that maternal ivacaftor therapy produce low levels in milk. An international survey of cystic fibrosis centers found no adverse effects in breastfed infants of mothers taking these drugs. A task force respiratory experts from Europe, Australia and New Zealand found that these drugs are probably safe during breastfeeding.[1] One breastfed infant had transient elevations in bilirubin and liver enzymes during maternal therapy that could not definitively be attributed to the drugs in breastmilk. Until more data are available, monitoring of infant bilirubin and liver enzymes might be advisable during breastfeeding with maternal ivacaftor therapy. Examination of breastfed infants for cataracts has also been recommended.[2]

PMID:30507114 | Bookshelf:NBK534421

2021 Apr 19. Drugs and Lactation Database (LactMed) [Internet]. Bethesda (MD): National Library of Medicine (US); 2006–.

ABSTRACT

Information from one maternal-infant pair with ivacaftor and lumacaftor indicates that maternal ivacaftor therapy produce low levels in milk. An international survey of cystic fibrosis centers found no adverse effects in breastfed infants of mothers taking these drugs. A task force respiratory experts from Europe, Australia and New Zealand found that these drugs are probably safe during breastfeeding.[1] One breastfed infant had transient elevations in bilirubin and liver enzymes during maternal therapy that could not definitively be attributed to the drugs in breastmilk. Until more data are available, monitoring of infant bilirubin and liver enzymes might be advisable during breastfeeding with maternal tezacaftor and ivacaftor therapy. Examination of breastfed infants for cataracts has also been recommended.[2]

PMID:30489718 | Bookshelf:NBK534420

2021 Apr 19. Drugs and Lactation Database (LactMed) [Internet]. Bethesda (MD): National Library of Medicine (US); 2006–.

ABSTRACT

Information from one maternal-infant pair with ivacaftor and lumacaftor indicates that maternal ivacaftor therapy produce low levels in milk. An international survey of cystic fibrosis centers found no adverse effects in breastfed infants of mothers taking these drugs. A task force respiratory experts from Europe, Australia and New Zealand found that these drugs are probably safe during breastfeeding.[1] One breastfed infant had transient elevations in bilirubin and liver enzymes during maternal therapy that could not definitively be attributed to the drugs in breastmilk. Until more data are available, monitoring of infant bilirubin and liver enzymes might be advisable during breastfeeding with maternal lumacaftor and ivacaftor therapy. Examination of breastfed infants for cataracts has also been recommended.[2]

PMID:30000992 | Bookshelf:NBK513062

2025 Feb 7. In: Feingold KR, Anawalt B, Blackman MR, Boyce A, Chrousos G, Corpas E, de Herder WW, Dhatariya K, Dungan K, Hofland J, Kalra S, Kaltsas G, Kapoor N, Koch C, Kopp P, Korbonits M, Kovacs CS, Kuohung W, Laferrère B, Levy M, McGee EA, McLachlan R, New M, Purnell J, Sahay R, Shah AS, Singer F, Sperling MA, Stratakis CA, Trence DL, Wilson DP, editors. Endotext [Internet]. South Dartmouth (MA): MDText.com, Inc.; 2000–.

ABSTRACT

In this chapter, indications for screening for diabetes mellitus are reviewed. Criteria for diagnosis are fasting plasma glucose ≥ 126 mg/dl (7.0 mmol/l) or random glucose ≥200 mg/dl (11.1 mmol/l) with hyperglycemic symptoms, hemoglobin A1c (HbA1c) ≥6.5%, and oral glucose tolerance testing (OGTT) 2-h glucose ≥200 mg/dl (11.1 mmol/l) after 75 g of glucose. One-step and two-step strategies for diagnosing gestational diabetes using pregnancy-specific criteria as well as use of the 2-h 75-g OGTT for the postpartum testing of women with gestational diabetes (4-12 weeks after delivery) are described. Testing for other forms of diabetes with unique features are reviewed, including the recommendation to use the 2-h 75 g OGTT to screen for cystic fibrosis-related diabetes and post-transplantation diabetes, fasting glucose test for HIV positive individuals, and genetic testing for monogenic diabetes syndromes including neonatal diabetes and maturity-onset diabetes of the young (MODY). Elevated measurements of pancreatic islet autoantibodies (e.g., to the 65-KDa isoform of glutamic acid decarboxylase (GAD65), tyrosine phosphatase related islet antigen 2 (IA-2), insulin (IAA), and zinc transporter (ZnT8)) suggest autoimmune type 1 diabetes (vs type 2 diabetes). IAA is primarily measured in youth. The use of autoantibody testing in diabetes screening programs is recommended in first degree relatives of an individual with type 1 diabetes or in research protocols. C-peptide measurements can be helpful in identifying those who have type 1 diabetes (low or undetectable c-peptide) from those who may have type 2 or monogenic diabetes. For complete coverage of all related areas of Endocrinology, please visit our on-line FREE web-text, WWW.ENDOTEXT.ORG.

PMID:25905219 | Bookshelf:NBK278985

2001 Mar 26 [updated 2022 Nov 10]. In: Adam MP, Everman DB, Mirzaa GM, Pagon RA, Wallace SE, Bean LJH, Gripp KW, Amemiya A, editors. GeneReviews® [Internet]. Seattle (WA): University of Washington, Seattle; 1993–2022.

ABSTRACT

CLINICAL CHARACTERISTICS: Cystic fibrosis (CF) is a multisystem disease affecting epithelia of the respiratory tract, exocrine pancreas, intestine, hepatobiliary system, and exocrine sweat glands. Morbidities include recurrent sinusitis and bronchitis, progressive obstructive pulmonary disease with bronchiectasis, exocrine pancreatic deficiency and malnutrition, pancreatitis, gastrointestinal manifestations (meconium ileus, rectal prolapse, distal intestinal obstructive syndrome), liver disease, diabetes, male infertility due to hypoplasia or aplasia of the vas deferens, and reduced fertility or infertility in some women. Pulmonary disease is the major cause of morbidity and mortality in CF.

DIAGNOSIS/TESTING: The diagnosis of CF is established in a proband with:

1. Elevated immunoreactive trypsinogen on newborn screen, signs and/or symptoms suggestive of CF, or family history of CF; AND

2. Evidence of an abnormality in cystic fibrosis transmembrane conductance regulator (CFTR) function: sweat chloride ≥60 mmol/L on sweat chloride testing, biallelic CFTR CF-causing pathogenic variants, or nasal transmembrane epithelial potential difference measurement consistent with CF.

MANAGEMENT: Treatment of manifestations – targeted therapy: CFTR modulator therapy is available for individuals with responsive CFTR variants.

Supportive care: Newborns: management by a CF specialist or CF care center; airway clearance instruction; encouraging feeding with breast milk; routine vaccinations; contact precautions with every encounter; antibiotics for bacterial suppression and treatment; nutrition management; pancreatic enzyme replacement; nutrient-dense food and supplements; fat-soluble vitamin supplements; laxative treatment as needed with surgical management for bowel obstruction; and salt and water supplementation.

After the newborn period: airway clearance; pulmonary treatment (bronchodilator, hypertonic saline, dornase alfa, airway clearance, inhaled corticosteroids and/or long-acting beta agonist, and aerosolized antibiotic); standard treatments for pneumothorax or hemoptysis; double lung transplant for those with advanced lung disease; routine vaccinations including influenza; contact precautions; antibiotics for bacterial suppression and treatment; antibiotics and/or surgical intervention for nasal/sinus symptoms; nutrition management; pancreatic enzyme replacement; nutrient-dense food and supplements; fat-soluble vitamin supplements; laxative treatment as needed with surgical management for bowel obstruction; standard treatments for gastroesophageal reflux disease; oral ursodiol for biliary sludging/obstruction; liver transplant when indicated; management of CF-related diabetes mellitus by an endocrinologist; assisted reproductive technologies (ART) for infertility; salt and water supplementation; standard treatments for associated mental health issues.

Surveillance: Frequent assessment by a CF specialist to monitor for new or worsening manifestations; pulmonary function testing frequently after age five years; chest x-ray or chest CT examination to assess for bronchiectasis every two years or as needed; cultures of respiratory tract secretions at least every three months; non-tuberculosis mycobacterium culture and serum IgE annually or as indicated; annual CBC with differential; annual ENT assessment; monitoring growth and GI manifestations at each visit; fecal elastase as needed; annual serum vitamin A, D, E, and PT (as a marker of vitamin K); annual liver function tests; annual random glucose, annual two-hour glucose tolerance test beginning at age ten years; DXA scan as needed in adolescence; infertility assessment as needed; annual electrolytes, BUN, and creatinine; annual assessment of depression and anxiety.

Agents/circumstances to avoid: Environmental smoke, exposure to respiratory infections, dehydration.

Evaluation of relatives at risk: Molecular genetic testing of at-risk sibs (if the pathogenic variants in the family are known) or sweat chloride testing of at-risk sibs (if the pathogenic variants in the family are not known) to identify as early as possible those who should be referred to a CF center for initiation of early treatment.

GENETIC COUNSELING: CF is inherited in an autosomal recessive manner. If both parents are known to be heterozygous for a CFTR pathogenic variant, each sib of an affected individual has at conception a 25% chance of being affected, a 50% chance of being heterozygous, and a 25% chance of inheriting neither of the familial pathogenic variants. Once the CFTR pathogenic variants have been identified in an affected family member, targeted heterozygote testing for at-risk relatives and prenatal/preimplantation genetic testing for CF are possible.

PMID:20301428 | Bookshelf:NBK1250