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Methods in Molecular Biology (Clifton,... 2022Microarrays are broadly used in the omic investigation and have several areas of applications in biology and medicine, providing a significant amount of data for a...
Microarrays are broadly used in the omic investigation and have several areas of applications in biology and medicine, providing a significant amount of data for a single experiment. Different kinds of microarrays are available, identifiable by characteristics such as the type of probes, the surface used as support, and the method used for the target detection. To better deal with microarray datasets, the development of microarray data analysis protocols simple to use as well as able to produce accurate reports, and comprehensible results arise. The object of this paper is to provide a general protocol showing how to choose the best software tool to analyze microarray data, allowing to efficiently figure out genomic/pharmacogenomic biomarkers.
Topics: Data Analysis; Gene Expression Profiling; Genomics; Microarray Analysis; Oligonucleotide Array Sequence Analysis; Software
PubMed: 34902134
DOI: 10.1007/978-1-0716-1839-4_17 -
Prenatal Diagnosis May 2022The research and clinical use of genome-wide sequencing for prenatal diagnosis of fetuses at risk for genetic disorders have rapidly increased in recent years. Current... (Review)
Review
The research and clinical use of genome-wide sequencing for prenatal diagnosis of fetuses at risk for genetic disorders have rapidly increased in recent years. Current data indicate that the diagnostic rate is comparable and for certain indications higher than that of standard testing by karyotype and chromosomal microarray. Responsible clinical implementation and diagnostic use of prenatal sequencing depends on standardized laboratory practices and detailed pre-test and post-test counseling. This Updated Position Statement on behalf of the International Society for Prenatal Diagnosis recommends best practices for the clinical use of prenatal exome and genome sequencing from an international perspective. We include several new points for consideration by researchers and clinical service and laboratory providers.
Topics: Exome; Female; Humans; Karyotyping; Microarray Analysis; Pregnancy; Prenatal Diagnosis; Exome Sequencing
PubMed: 35583085
DOI: 10.1002/pd.6157 -
American Journal of Obstetrics and... Sep 2023Emerging studies suggest that whole genome sequencing provides additional diagnostic yield of genomic variants when compared with chromosomal microarray analysis in the...
BACKGROUND
Emerging studies suggest that whole genome sequencing provides additional diagnostic yield of genomic variants when compared with chromosomal microarray analysis in the etiologic diagnosis of infants and children with suspected genetic diseases. However, the application and evaluation of whole genome sequencing in prenatal diagnosis remain limited.
OBJECTIVE
This study aimed to evaluate the accuracy, efficacy, and incremental yield of whole genome sequencing in comparison with chromosomal microarray analysis for routine prenatal diagnosis.
STUDY DESIGN
In this prospective study, a total of 185 unselected singleton fetuses with ultrasound-detected structural anomalies were enrolled. In parallel, each sample was subjected to whole genome sequencing and chromosomal microarray analysis. Aneuploidies and copy number variations were detected and analyzed in a blinded fashion. Single nucleotide variations and insertions and deletions were confirmed by Sanger sequencing, and trinucleotide repeats expansion variants were verified using polymerase chain reaction plus fragment-length analysis.
RESULTS
Overall, genetic diagnoses using whole genome sequencing were obtained for 28 (15.1%) cases. Whole genome sequencing not only detected all these aneuploidies and copy number variations in the 20 (10.8%) diagnosed cases identified by chromosomal microarray analysis, but also detected 1 case with an exonic deletion of COL4A2 and 7 (3.8%) cases with single nucleotide variations or insertions and deletions. In addition, 3 incidental findings were detected including an expansion of the trinucleotide repeat in ATXN3, a splice-sites variant in ATRX, and an ANXA11 missense mutation in a case of trisomy 21.
CONCLUSION
Compared with chromosomal microarray analysis, whole genome sequencing increased the additional detection rate by 5.9% (11/185). Using whole genome sequencing, we detected not only aneuploidies and copy number variations, but also single nucleotide variations and insertions and deletions, trinucleotide repeat expansions, and exonic copy number variations with high accuracy in an acceptable turnaround time (3-4 weeks). Our results suggest that whole genome sequencing has the potential to be a new promising prenatal diagnostic test for fetal structural anomalies.
Topics: Pregnancy; Female; Infant; Child; Humans; Prospective Studies; DNA Copy Number Variations; Ultrasonography, Prenatal; Pregnancy Trimester, First; Prenatal Diagnosis; Aneuploidy; Whole Genome Sequencing; Microarray Analysis; Chromosome Aberrations
PubMed: 36907537
DOI: 10.1016/j.ajog.2023.03.005 -
American Journal of Human Genetics Aug 2021Chromosomal aberrations including structural variations (SVs) are a major cause of human genetic diseases. Their detection in clinical routine still relies on standard...
Chromosomal aberrations including structural variations (SVs) are a major cause of human genetic diseases. Their detection in clinical routine still relies on standard cytogenetics. Drawbacks of these tests are a very low resolution (karyotyping) and the inability to detect balanced SVs or indicate the genomic localization and orientation of duplicated segments or insertions (copy number variant [CNV] microarrays). Here, we investigated the ability of optical genome mapping (OGM) to detect known constitutional chromosomal aberrations. Ultra-high-molecular-weight DNA was isolated from 85 blood or cultured cells and processed via OGM. A de novo genome assembly was performed followed by structural variant and CNV calling and annotation, and results were compared to known aberrations from standard-of-care tests (karyotype, FISH, and/or CNV microarray). In total, we analyzed 99 chromosomal aberrations, including seven aneuploidies, 19 deletions, 20 duplications, 34 translocations, six inversions, two insertions, six isochromosomes, one ring chromosome, and four complex rearrangements. Several of these variants encompass complex regions of the human genome involved in repeat-mediated microdeletion/microduplication syndromes. High-resolution OGM reached 100% concordance compared to standard assays for all aberrations with non-centromeric breakpoints. This proof-of-principle study demonstrates the ability of OGM to detect nearly all types of chromosomal aberrations. We also suggest suited filtering strategies to prioritize clinically relevant aberrations and discuss future improvements. These results highlight the potential for OGM to provide a cost-effective and easy-to-use alternative that would allow comprehensive detection of chromosomal aberrations and structural variants, which could give rise to an era of "next-generation cytogenetics."
Topics: Chromosome Aberrations; Chromosome Disorders; Chromosome Mapping; Cytogenetic Analysis; DNA Copy Number Variations; Genome, Human; Humans; Karyotyping; Microarray Analysis
PubMed: 34237280
DOI: 10.1016/j.ajhg.2021.05.012 -
Advances in Biochemical... 2021Glycan (or carbohydrate) arrays have become an essential tool in glycomics, providing fast and high-throughput data on protein-carbohydrate interactions with small...
Glycan (or carbohydrate) arrays have become an essential tool in glycomics, providing fast and high-throughput data on protein-carbohydrate interactions with small amounts of carbohydrate ligands. The general concepts of glycan arrays have been adopted from other microarray technologies such as those used for nucleic acid and proteins. However, carbohydrates have presented their own challenges, in particular in terms of access to glycan probes, linker attachment chemistries and analysis, which will be reviewed in this chapter. As more and more glycan probes have become available through chemical and enzymatic synthesis and robust linker chemistries have been developed, the applications of glycan arrays have dramatically increased over the past 10 years, which will be illustrated with recent examples.
Topics: Glycomics; Ligands; Microarray Analysis; Polysaccharides; Technology
PubMed: 31907566
DOI: 10.1007/10_2019_112 -
Genes Mar 2021In 1959, 63 years after the death of John Langdon Down, Jérôme Lejeune discovered trisomy 21 as the genetic reason for Down syndrome. Screening for Down syndrome has... (Review)
Review
In 1959, 63 years after the death of John Langdon Down, Jérôme Lejeune discovered trisomy 21 as the genetic reason for Down syndrome. Screening for Down syndrome has been applied since the 1960s by using maternal age as the risk parameter. Since then, several advances have been made. First trimester screening, combining maternal age, maternal serum parameters and ultrasound findings, emerged in the 1990s with a detection rate (DR) of around 90-95% and a false positive rate (FPR) of around 5%, also looking for trisomy 13 and 18. With the development of high-resolution ultrasound, around 50% of fetal anomalies are now detected in the first trimester. Non-invasive prenatal testing (NIPT) for trisomy 21, 13 and 18 is a highly efficient screening method and has been applied as a first-line or a contingent screening approach all over the world since 2012, in some countries without a systematic screening program. Concomitant with the rise in technology, the possibility of screening for other genetic conditions by analysis of cfDNA, such as sex chromosome anomalies (SCAs), rare autosomal anomalies (RATs) and microdeletions and duplications, is offered by different providers to an often not preselected population of pregnant women. Most of the research in the field is done by commercial providers, and some of the tests are on the market without validated data on test performance. This raises difficulties in the counseling process and makes it nearly impossible to obtain informed consent. In parallel with the advent of new screening technologies, an expansion of diagnostic methods has begun to be applied after invasive procedures. The karyotype has been the gold standard for decades. Chromosomal microarrays (CMAs) able to detect deletions and duplications on a submicroscopic level have replaced the conventional karyotyping in many countries. Sequencing methods such as whole exome sequencing (WES) and whole genome sequencing (WGS) tremendously amplify the diagnostic yield in fetuses with ultrasound anomalies.
Topics: Chromosome Disorders; Female; Genetic Testing; Humans; Microarray Analysis; Pregnancy; Prenatal Diagnosis
PubMed: 33805390
DOI: 10.3390/genes12040501 -
Epigenetics Dec 2023DNA methylation, one of the best characterized epigenetic marks in the human genome, plays a pivotal role in gene transcription regulation and other biological processes...
DNA methylation, one of the best characterized epigenetic marks in the human genome, plays a pivotal role in gene transcription regulation and other biological processes in humans. On top of that, the DNA methylome undergoes profound changes in cancer and other disorders. However, large-scale and population-based studies are limited by high costs and the need for considerable expertise in data analysis for whole-genome bisulphite-sequencing methodologies. Following the success of the EPIC DNA methylation microarray, the newly developed Infinium HumanMethylationEPIC version 2.0 (900K EPIC v2) is now available. This new array contains more than 900,000 CpG probes covering the human genome and excluding masked probes from the previous version. The 900K EPIC v2 microarray adds more than 200,000 probes covering extra DNA cis-regulatory regions such as enhancers, super-enhancers and CTCF binding regions. Herein, we have technically and biologically validated the new methylation array to show its high reproducibility and consistency among technical replicates and with DNA extracted from FFPE tissue. In addition, we have hybridized primary normal and tumoural tissues and cancer cell lines from different sources and tested the robustness of the 900K EPIC v2 microarray when analysing the different DNA methylation profiles. The validation highlights the improvements offered by the new array and demonstrates the versatility of this updated tool for characterizing the DNA methylome in human health and disease.
Topics: Humans; DNA Methylation; Epigenome; Reproducibility of Results; Microarray Analysis; Cell Line
PubMed: 36871255
DOI: 10.1080/15592294.2023.2185742 -
Annals of Medicine Dec 2023To evaluate the clinical utility of chromosomal microarray analysis (CMA) and whole exome sequencing (WES) in foetuses with oligohydramnios.
OBJECTIVES
To evaluate the clinical utility of chromosomal microarray analysis (CMA) and whole exome sequencing (WES) in foetuses with oligohydramnios.
METHODS
In this retrospective study, 126 fetuses with oligohydramnios at our centre from 2018 to 2021 were reviewed. The results of CMA and WES were analysed.
RESULTS
One hundred and twenty-four cases underwent CMA and 32 cases underwent WES. The detection rate of pathogenic/likely pathogenic (P/LP) copy number variant (CNV) by CMA was 1.6% (2/124). WES revealed P/LP variants in 21.8% (7/32) of the foetuses. Six (85.7%, 6/7) foetuses showed an autosomal recessive inheritance pattern. Three (42.9%, 3/7) variants were involved in the renin-angiotensin-aldosterone system (RAAS), which are the known genetic causes of autosomal recessive renal tubular dysgenesis (ARRTD).
CONCLUSION
CMA has low diagnostic utility for oligohydramnios, while WES offers obvious advantages in improving the detection rate. WES should be recommended for fetuses with oligohydramnios.
Topics: Pregnancy; Female; Humans; Retrospective Studies; Exome Sequencing; Oligohydramnios; Microarray Analysis; Fetus; Prenatal Diagnosis
PubMed: 37243546
DOI: 10.1080/07853890.2023.2215539 -
Advances in Biochemical... 2024Microarrays are widely utilized in bioanalysis. Electrochemical biosensing techniques are often applied in microarray-based assays because of their simplicity, low cost,... (Review)
Review
Microarrays are widely utilized in bioanalysis. Electrochemical biosensing techniques are often applied in microarray-based assays because of their simplicity, low cost, and high sensitivity. In such systems, the electrodes and sensing elements are arranged in arrays, and the target analytes are detected electrochemically. These sensors can be utilized for high-throughput bioanalysis and the electrochemical imaging of biosamples, including proteins, oligonucleotides, and cells. In this chapter, we summarize recent progress on these topics. We categorize electrochemical biosensing techniques for array detection into four groups: scanning electrochemical microscopy, electrode arrays, electrochemiluminescence, and bipolar electrodes. For each technique, we summarize the key principles and discuss the advantages, disadvantages, and bioanalysis applications. Finally, we present conclusions and perspectives about future directions in this field.
Topics: Biosensing Techniques; Electrochemical Techniques; Microarray Analysis; Electrodes; Humans
PubMed: 37306698
DOI: 10.1007/10_2023_229 -
American Journal of Medical Genetics.... Dec 2020The aim of this study was to perform 22q11.2 deletion screening and chromosomal microarray analysis (CMA) in individuals clinically diagnosed with craniofacial... (Review)
Review
The aim of this study was to perform 22q11.2 deletion screening and chromosomal microarray analysis (CMA) in individuals clinically diagnosed with craniofacial microsomia (CFM) and review previously published cases of CFM with genomic imbalances. It included 54 individuals who were evaluated by a clinical geneticist. Copy number variants (CNVs) in the 22q11.2 region were investigated by multiplex ligation-dependent probe amplification (MLPA) for all individuals. The CMA was performed only for individuals with additional major features. MLPA revealed pathogenic CNVs at the 22q11 region in 3/54 (5.6%) individuals. CMA revealed pathogenic CNVs in 4/17 (23.5%) individuals, including the three CNVs at the 22q11 region also detected by MLPA, and CNVs classified as variants of unknown significance (VOUS) in 4/17 (23.5%) individuals. Pathogenic alterations were found at the 2p12, 5p15, 13q13, and 22q11 regions. VOUS were found at 3q29, 5q22.2, 5q22.1, and 9p22 regions. All individuals with pathogenic alterations presented additional major features, including congenital heart disease (CHD). The literature review revealed pathogenic CNVs in 17/193 (8.8%) individuals and most of them also presented additional major features, such as CHD, renal anomalies, or developmental delay. In conclusion, CNVs should be investigated in patients with CFM and additional major features.
Topics: DNA Copy Number Variations; Genomics; Goldenhar Syndrome; Heart Defects, Congenital; Humans; Microarray Analysis
PubMed: 33215817
DOI: 10.1002/ajmg.c.31857