Whole-genome Technologies Research Articles

Mozambican Coffea accessions from Ibo and Quirimba Islands: identification and geographical distribution.

Mozambique does not have a tradition of farming Coffea arabica or Coffea canephora, the two species that dominate the worldwide coffee market. However, native coffee plants have been growing spontaneously and in some cases cultivated in the Ibo and Quirimba islands in the north of the country and Inhambane province in the south. Historically there has been confusion over the precise taxonomic classification of these indigenous coffee plants, with different botanists identifying the species as C. racemosa, C. zanguebariae or various synonyms of both. The present research aims to clarify the subject and provide new information on these little-described coffee species which may prove valuable as new breeding material for future cultivars, something that is sorely needed to face the present and future challenges of coffee production. Leaf samples were collected from 40 accessions from Ibo Island, Quirimba Island and Inhambane province. The samples were sequenced by whole-genome technology and WGS reads were filtered to identify relevant SNP variants. Diversity among the samples was assessed by PCA, and a phylogenetic tree including several Coffea species was built using additional data available in public databases. Experimental data confirm the presence of C. zanguebariae as the only coffee species present in both Ibo and Quirimba Islands, while it appears that C. racemosa is exclusive to the southern Inhambane province. The present research provides the most detailed analysis so far on the genetic identity of the traditional Mozambican coffee crops. This is the prerequisite for undertaking further scientific studies on these almost unknown coffee species and for starting agronomic development programs for the economic revival of Ibo and Quirimba islands based on coffee cultivation. Furthermore, these species could provide much-needed genetic material for the breeding of new hybrids with the two main commercial coffee species.

P-718 Preimplantation genetic testing in Belgium: recommendations for the genetic centres

Abstract Study question How do genetic centres in Belgium apply international guidelines on preimplantation genetic testing (PGT)? Summary answer We present the national consensus on how to practice PGT, starting from initial patient uptake and embryo selection to follow-up of pregnancies. What is known already PGT includes PGT-M for monogenic disorders, PGT-SR for structural rearrangements and PGT-A for aneuploidy screening. The application of whole-genome technologies to trophectoderm biopsies for PGT-M and PGT-SR/A has evidenced the high prevalence of mosaicism due to chromosome segregation errors during the first mitotic divisions, making biopsy results interpretation and embryo transfer policy more challenging and complex. Guidelines from several international societies have been published in recent years to leverage the standardization of the whole PGT service. Although these are based on expertise and continuously acquiring evidence, it is widely recognized that variations in local and national regulations diversify PGT practices. Study design, size, duration Recommendations regarding PGT indications, patient counselling, embryo transfer policy, reporting, quality and pregnancy follow-up have been built to harmonize PGT services nationally. With a special focus on mosaicism, aiming to balance the highest chance for a pregnancy with the lowest risk for a chromosomally abnormal ongoing pregnancy or child. Participants/materials, setting, methods The Belgian PGT working group consists of laboratory geneticists, clinical geneticists and IVF specialists from eight nationally accredited centres. The group operates under the BeSHG umbrella and meets quarterly to formulate opinions and statements on PGT practice with the main goal of guaranteeing a high standard of care, exchange knowledge and implement a harmonized workflow. The Belgian social security system provides reimbursement of six genetic testing cycles for all PGT-M/SR patients but not for PGT-A. Main results and the role of chance PGT is offered for all monogenic and chromosomal disorders, if the causal genetic variants are known and documented. PGT for HLA-typing is allowed for the therapeutic benefit of an existing child after couple's psychological evaluation. Aneuploidy screening can be offered to specific patient groups to increase IVF success rate. However, social sexing and testing for non-medical or eugenic purposes is prohibited. At intake, the couple is counselled about the genetic aspect of the disease, psychological and financial aspects of PGT, applied methodology, including average success and misdiagnosis rate, and embryo transfer policies. Affected embryos, and embryos without diagnosis for PGT-M/SR are not transferred. For PGT-A (combined or not with PGT-M/SR), embryos are categorized as: (A) Euploid - suitable for transfer, if mosaicism is absent or below the detection threshold. (B) Mosaic transferable - suitable for transfer, but only following ranking and/or counselling and follow up, if mosaicism for any chromosome not described in (C) is detected; (C) Aneuploid or Mosaic - not suitable for transfer, if mosaicism of 8, 9, 13, 16, 18, 21 and X or full aneuploidy of any chromosome is detected. Non-invasive prenatal testing is strongly recommended to all women pregnant after PGT and is nationally reimbursed. Limitations, reasons for caution The practical recommendations, which are supplementary to the recently published ESHRE PGT recommendations, are based on expertise and data from the literature available at the time of preparation. As such, they will need regular reconsideration and an update or extension may follow when new solid scientific evidence arises. Wider implications of the findings As international recommendations represent a greatest common denominator over many local regulations, this work serves as example for drawing country-specific agreements for genetic centres. The process of consensus expert opinion formation on best practice may be applicable in other countries where PGT service is not overseen by a designated agency. Trial registration number Not applicable

Use of whole-genome analysis to study the effect of various quorum-sensing inhibitors on the biofilm formation of Lactobacillus fermentum

To explore the effects of different quorum sensing inhibitors (QSIs) on the biofilm formation of Lactobacillus fermentum, a high-production signal molecule AI-2 screened by the research group, was taken as the research object and subjected to various QSIs. Three QSIs, namely 100 μmol/L d-galactose, 200 μmol/L d-ribose, and furanone, could inhibit the AI-2 activity of L. fermentum and the biofilm formation in a certain concentration range but not significantly affect the growth of the strain. Scanning electron microscopy and fluorescence microscopy revealed that each QSI did not significantly affect the bacterial cell morphology in planktonic and biofilm states at the optimal inhibitory final concentration, although they reduced the adhesion of the strain. The expression of luxS, a key gene of quorum sensing, was downregulated. When biofilm production increased, QSIs were added, and the activity of the AI-2 was consistent with the change in biofilm production. Whole-genome technology revealed that QSIs inhibited the expression of the luxS, resulting in restriction of pyruvate synthesis and downregulation of the expression of genes such as gapA, pgmB, ribBA, and ribF, which in turn affected the transport and metabolism of carbohydrates and coenzymes in the strain and ultimately reduced the biofilm formation of L. fermentum.

A Tale of Native American Whole-Genome Sequencing and Other Technologies

Indigenous people from the American continent, or Native Americans, are underrepresented in the collective genomic knowledge. A minimal percentage of individuals in international databases belong to these important minority groups. Yet, the study of native American genomics is a growing field. In this work, we reviewed 56 scientific publications where ancient or contemporary DNA of Native Americans across the continent was studied by array, whole-exome, or whole-genome technologies. In total, 13,706 native Americans have been studied with genomic technologies, of which 1292 provided whole genome samples. Data availability is lacking, with barely 3.6% of the contemporary samples clearly accessible for further studies; in striking contrast, 96.3% of the ancient samples are publicly available. We compiled census data on the home countries and found that 607 indigenous groups are still missing representation in genomic datasets. By analyzing authorship of the published works, we found that there is a need for more involvement of the home countries as leads in indigenous genomic studies. We provide this review to aid in the design of future studies that aim to reduce the missing diversity of indigenous Americans.

Plasmids Shaped the Recent Emergence of the Major Nosocomial Pathogen Enterococcus faecium.

Enterococcus faecium is a gut commensal of humans and animals but is also listed on the WHO global priority list of multidrug-resistant pathogens. Many of its antibiotic resistance traits reside on plasmids and have the potential to be disseminated by horizontal gene transfer. Here, we present the first comprehensive population-wide analysis of the pan-plasmidome of a clinically important bacterium, by whole-genome sequence analysis of 1,644 isolates from hospital, commensal, and animal sources of E. faecium Long-read sequencing on a selection of isolates resulted in the completion of 305 plasmids that exhibited high levels of sequence modularity. We further investigated the entirety of all plasmids of each isolate (plasmidome) using a combination of short-read sequencing and machine-learning classifiers. Clustering of the plasmid sequences unraveled different E. faecium populations with a clear association with hospitalized patient isolates, suggesting different optimal configurations of plasmids in the hospital environment. The characterization of these populations allowed us to identify common mechanisms of plasmid stabilization such as toxin-antitoxin systems and genes exclusively present in particular plasmidome populations exemplified by copper resistance, phosphotransferase systems, or bacteriocin genes potentially involved in niche adaptation. Based on the distribution of k-mer distances between isolates, we concluded that plasmidomes rather than chromosomes are most informative for source specificity of E. faeciumIMPORTANCEEnterococcus faecium is one of the most frequent nosocomial pathogens of hospital-acquired infections. E. faecium has gained resistance against most commonly available antibiotics, most notably, against ampicillin, gentamicin, and vancomycin, which renders infections difficult to treat. Many antibiotic resistance traits, in particular, vancomycin resistance, can be encoded in autonomous and extrachromosomal elements called plasmids. These sequences can be disseminated to other isolates by horizontal gene transfer and confer novel mechanisms to source specificity. In our study, we elucidated the total plasmid content, referred to as the plasmidome, of 1,644 E. faecium isolates by using short- and long-read whole-genome technologies with the combination of a machine-learning classifier. This was fundamental to investigate the full collection of plasmid sequences present in our collection (pan-plasmidome) and to observe the potential transfer of plasmid sequences between E. faecium hosts. We observed that E. faecium isolates from hospitalized patients carried a larger number of plasmid sequences compared to that from other sources, and they elucidated different configurations of plasmidome populations in the hospital environment. We assessed the contribution of different genomic components and observed that plasmid sequences have the highest contribution to source specificity. Our study suggests that E. faecium plasmids are regulated by complex ecological constraints rather than physical interaction between hosts.

Reconstruction of the Austronesian Diaspora in the Era of Genomics.

The Austronesian Diaspora is a 5,000-year account of how a small group of Taiwanese farmers expanded to occupy territories reaching halfway around the world. Reconstructing their detailed history has spawned many academic contests across many disciplines. An outline orthodox version has eventually emerged but still leaves many unanswered questions. The remarkable power of whole-genome technology has now been applied to people across the entire region. This review gives an account of this era of genetic investigation and discusses its many achievements, including revelation in detail of many unexpected patterns of population movement and the significance of this information for medical genetics.

Abstract P3-06-17: Unlocking the transcriptomic potential of formalin-fixed paraffin embedded breast cancer tissues for high-throughput genomic analysis

Abstract Background: Transcriptomic analyses of clinical samples can help improve our understanding of disease aetiology, drug effectiveness, assign molecular subtypes and derive prognostic signatures for clinical decision-making. The success of early microarray studies relied heavily on sample quality and predominantly fresh frozen (FF) tissues to generate reliably robust data. The emergence of next-generation microarray and sequencing-based technologies from formalin-fixed paraffin-embedded (FFPE) tissues provides an opportunity to study archival clinical tissues with long-term follow-up. Here we assess 9 technologies, which vary in resolution, cost and RNA requirements, with matched FF and FFPE tissues from the same patient. Methods: Sequential tumour biopsies were taken pre-treatment and on-treatment (at 14-days and 3-months) from 11 postmenopausal patients with oestrogen receptor positive breast cancer treated with 3 months of neoadjuvant letrozole. Half of each sample was snap frozen in liquid nitrogen and half was FFPE, RNA was extracted from both. Transcriptomic analyses were performed using 9 technologies: Illumina Beadarray, Affymetrix U133A, Affymetrix Clariom S, NanoString nCounter, AmpliSeq Transcriptome, Lexogen QuantSeq and IonXpress RNAseq, Tempo-Seq BioSpyder and Qiagen UPX3'. Results: Success rates for generating robust expression profiles from FFPE tissues were 100% all except the Illumina BeadChip (22%) and AmpliSeq Transcriptome (83%) , which varied by the age of tissue. With the total number and position of probes/primers/counts varying widely between approaches, in total 7305 genes were represented across all of the whole-genome technologies tested. Clear batch effects were evident when comparing data from FF and FFPE tissues and when comparing between different technologies. Standard batch correction approaches such as XPN and ComBat minimised technical bias effect and increased the correlations between matched samples (FF and FFPE) to R>0.9, irrespective of the technology used. When analysed by multi-dimensional scaling following batch correction, samples clustered by treatment time-point. When ranked by expression of 60 proliferation genes, reported by us to change with letrozole treatment, samples ordered again by time-point, consistent with our previous findings, and paired samples clustered together. Conclusions: · Robust gene expression profiles can be reliably generated from FFPE tissues and are comparable to those derived from FF tissue using established transcriptomic approaches. · A range of new technologies are available for the study of FFPE tissues; these vary in cost, resolution and RNA requirements to fit the user's needs. · Gene expression data from biologically similar studies, generated using different technologies, can be reliably integrated for robust meta-analysis, subject to appropriate batch correction analysis. Citation Format: Turnbull AK, Selli C, Martinez-Perez C, Fernando A, Renshaw L, Keys J, Figueroa JD, He X, Tanioka M, Munro A, Murphy L, Fawkes A, Clark R, Coutts A, Perou CM, Carey LA, Dixon JM, Sims AH. Unlocking the transcriptomic potential of formalin-fixed paraffin embedded breast cancer tissues for high-throughput genomic analysis [abstract]. In: Proceedings of the 2018 San Antonio Breast Cancer Symposium; 2018 Dec 4-8; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2019;79(4 Suppl):Abstract nr P3-06-17.

Selective vulnerability in neurodegenerative diseases.

Neurodegenerative diseases have two general characteristics that are so fundamental we usually take them for granted. The first is that the pathology associated with the disease only affects particular neurons ('selective neuronal vulnerability'); the second is that the pathology worsens with time and impacts more regions in a stereotypical and predictable fashion. The mechanisms underpinning selective neuronal and regional vulnerability have been difficult to dissect, but the recent application of whole-genome technologies, the development of mouse models that reproduce spatial and temporal features of the pathology, and the identification of intrinsic morphological, electrophysiological, and biochemical properties of vulnerable neurons are beginning to shed some light on these fundamental features of neurodegenerative diseases. Here we detail our emerging understanding of the underlying biology of selective neuronal vulnerability and outline some of the areas in which our understanding is incomplete.

Mapping of chromosomal balanced rearrangements by whole-genome sequencing identifies genes involved in epilepsy

Objective: Epilepsy is a frequent neurologic condition, with a frequency of 1% in the population. Identification of genes involved in epilepsy has been challenged by the genetic heterogeneity, phenotypic variability and phenocopies. During the last years, new whole-genome technologies such as array-comparative genomic hybridization (aCGH) and next-generation sequencing (NGS) allowed the identification of copy-number variations (CNVs) and single nucleotide variations (SNVs) involved in this condition. An alternative strategy to uncover new genes in epilepsy is the molecular characterization of apparently-balanced chromosomal rearrangements (ABCRs). This approach relies on the fact that a disease-causing gene may be disrupted by the breakpoints or its expression may be affected by a position effect. Methods: We report the study of 3 patients carrying respectively a paracentric inversion inv(2)(q22;q32.3) (P1), a pericentric inversion inv(2)(p12q22) (P2), and a balanced translocation t(11;15)(p14;q14) (P3) associated with epilepsy, intellectual disability and malformations for P3. Whole-genome paired-end sequencing, coupled with Sanger sequencing, allowed the characterization of ABCRs at base-pair level in all three patients. These results were also confirmed by FISH. Results: We demonstrated the disruption of three genes: MBD5 (2q23.1) in P1 and P2, M1AP (2p13.1) in P1 and MEIS2 (15q14) in P3. Expression studies by RT-qPCR showed a reduced expression of MBD5 in both patients P1 and P2. MBD5 is associated with intellectual disability, severe language impairment, epilepsy, and autistic spectrum disorders. Disruption of MBD5 appears to be responsible for the phenotype of patients P1 and P2. Disruption of MEIS2 in patient P3 contributes to her malformations and intellectual disability but has never been described in epilepsy to our knowledge. Conclusion: MEIS2 may be a new candidate gene in epilepsy, but a position effect on neighboring genes may not be excluded. Ongoing expression studies may help to confirm these hypotheses.

Abstract 4655: Molecular Inversion Probe analysis using OncoScan™ FFPE Assay Kit to detect copy number aberrations and somatic mutations in lung tumor DNA samples from formalin-fixed paraffin-embedded (FFPE) tissue

Abstract DNA copy number (CN) studies hold great promise for the discovery of clinical biomarkers to predict disease course, recurrence risk, and response to therapy. The molecular characterization of a tumor genome across many samples helps to classify cancers in a biologically and clinically relevant manner. While exciting results have been found with genes already known to be involved in key pathways, confirming early results and genome-wide testing requires large numbers of well-characterized clinical samples. A vast collection of hundreds of millions of stored FFPE samples already exists. Unfortunately, many genomic assays fail to produce high-quality CN and genotype data from FFPE samples, given the degradation and chemical changes to the DNA and the small quantity obtained from tiny tissue samples. The higher rate of sequencing artifacts and genotyping failures in FFPE samples restricts the application of these promising whole-genome scanning technologies to the limited number of fresh-frozen samples. OncoScan™ FFPE Assay Kit is designed to interrogate the whole genome for copy number aberrations (CNAs), loss of heterozygosity (LOH), and selected somatic mutations (SMs) and captures the alleles of over 220,000 SNPs at carefully selected genomic locations. These SNPs are evenly distributed across the genome and with increased density within ∼900 cancer-related genes. Based on Molecular Inversion Probe (MIP) technology, several OncoScan Assay Kit features make it highly suitable for the analysis of FFPE tissue-derived DNA. The assay uses only 80 ng input DNA with no requirement for amplification of the genomic DNA; rather, the probe itself is amplified, leading to a high signal-to-noise ratio. The entire assay can be run such that results can be obtained within 48 hours of gDNA extraction. Cancer sample data are complex because each sample is inherently mosaic, comprised of a mixture of normal cells along with one or multiple tumor clones. OncoScan FFPE Assay Kit includes a component algorithm that specifically addresses the issue of normal contamination in the tumor sample. In this study, we will describe the characterization of genomic variations in a set of 67 lung tumor samples collected in collaboration with Cancer Research UK (CRUK). From each sample, 80 ng FFPE gDNA has been extracted and purified as input to OncoScan Assay Kit. Collectively, the tumor genomes showed frequent CN gains on chromosomes 1q, 5p, 6p, 7, 8q, and 17q and frequent CN losses on chromosomes 6q and 17p. The number of structural aberrations per sample ranged from 3 to 340, with an average of 94. The assay simultaneously interrogates 74 SMs of interest using a panel of 64 MIPs. Forty-nine samples had at least 1 SM call (1 sample having a maximum of 4). Citation Format: Ron Sapolsky, Anju Shukla, Sumathi Venkatapathy, Chuan Chen, Carsten Bruckner, Vicky Huynh, Liansen Liu, Xuan Shen, Kent Suyenaga, Patrick Weaver, Wai Wu, Bitao Liu, Matt Ghent, Benjamin Bolstad, Farooq Siddiqui, Diana Abdueva, Mirjana Alvi, Eric Fung, Jeanette Schmidt, Lawrence Greenfield. Molecular Inversion Probe analysis using OncoScan™ FFPE Assay Kit to detect copy number aberrations and somatic mutations in lung tumor DNA samples from formalin-fixed paraffin-embedded (FFPE) tissue. [abstract]. In: Proceedings of the 105th Annual Meeting of the American Association for Cancer Research; 2014 Apr 5-9; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2014;74(19 Suppl):Abstract nr 4655. doi:10.1158/1538-7445.AM2014-4655

Genome-wide profiling of changes in gene expression in response to infection of the japonica rice variety Yunyin by Magnaporthe oryzae

Rice blast, caused by the fungus Magnaporthe oryzae, is one of the diseases most responsible for significantly decreasing the yield and quality of commercially grown rice. This study investigated the blast resistance response of japonica rice variety Yunyin (YY) treated with the Sichuan-43 isolate of M. oryzae. Seedlings of YY exhibited stronger resistance to blast than those of Lijiangxintuanheigu (LTH). The gene expression profile of YY treated with Sichuan-43 was determined using whole-genome microarray technology. Bioinformatics was used to identify putative resistance-related genes from the large number of genes assayed. Five candidate genes were further characterized by gene ontology classification analysis and pathway enrichment analysis, and were then integrated into various types of gene network regulation diagrams. Systematic bioinformatic analysis of the microarray provided a transcriptome map of YY, which helped to elucidate the mechanisms involved in blast resistance. Our results enhance the current understanding of the effects of rice blast resistance genes at the transcription level, and will facilitate further exploration of the molecular mechanism of blast resistance in YY.

The genomic map of breast cancer: which roads lead to better targeted therapies?

Recent advances in whole-genome technologies have supplied the field of cancer research with an overwhelming amount of molecular data. Improvements in massively parallel sequencing approaches have led to logarithmic decreases in costs, and so these methods are becoming almost commonplace in the analysis of clinical trials and other cohorts of interest. Furthermore, whole-transcriptome quantification by RNA sequencing is quickly replacing microarrays. However, older chip-based methodologies such as comparative genomic hybridization and single-nucleotide polymorphism arrays have benefited from this technological explosion and are now so accessible that they can be employed in increasingly larger cohorts of patients. The study of breast cancer lends itself particularly well to these technologies. It is the most commonly diagnosed neoplasm in women, giving rise to nearly 230,000 new cases each year. Many patients are given a diagnosis of early-stage disease, for which surgery is the standard of care. These attributes result in excellent availability of tissues for whole-genome/transcriptome analysis. The Cancer Genome Atlas project has generated comprehensive catalogs of publically available genomic breast cancer data. In addition, other studies employing the power of genomic technologies in medium to large cohorts were recently published. These data are now publically available for the generation of novel hypotheses. However, these studies differed in the methods, patient cohorts, and analytical techniques employed and represent complementary snapshots of the molecular underpinnings of breast cancer. Here, we will discuss the convergences and divergences of these reports as well as the scientific and clinical implications of their findings.

Clinical Application of Targeted and Genome-Wide Technologies: Can we Predict Treatment Responses in Chronic Lymphocytic Leukemia?

Chronic lymphocytic leukemia (CLL) is low-grade lymphoma of mature B cells and it is considered to be the most common type of hematological malignancy in the western world. CLL is characterized by a chronically relapsing course and clinical and biological heterogeneity. Many patients do not require any treatment for years. Although important progress has been made in the treatment of CLL, none of the conventional treatment options are curative. Recurrent chromosomal abnormalities have been identified and are associated with prognosis and pathogenesis of the disease. More recently, unbiased genome-wide technologies have identified multiple additional recurrent aberrations. The precise predictive value of these has not been established, but it is likely that the genetic heterogeneity observed at least partly reflects the clinical variability. The present article reviews our current knowledge of predictive markers in CLL using whole-genome technologies.

Genetics of Peripheral Artery Disease

Broadly defined, peripheral vascular disease refers to disease of the extracardiac blood vessels, including diseases of the arteries, veins, and lymphatics. Peripheral arterial disease (PAD) refers to disease affecting noncoronary arteries, but is most often used to describe disease of the arteries supplying the limbs. Peripheral arterial disease is most commonly due to atherosclerosis, but may also be secondary to cardiac or vascular embolism, vasculitis, hypercoagulopathy, vascular dissection, vascular compression syndromes, and other less common disorders. In addition, PADs include those characterized by fixed or dynamic stenoses, and aneurysmal disease such as abdominal aortic aneurysm, as well. In this review, we focus on atherosclerotic arterial occlusive disease affecting the vessels supplying blood flow to the lower extremities (PAD), and discuss our current understanding and the future directions of PAD genetics. PAD is a significant public health problem, and a major source of morbidity and mortality that affects ≈8 million Americans. PAD contributes to impaired quality of life (eg, intermittent claudication reducing mobility), morbidity (eg, nonhealing ulcers and ischemic rest pain), and mortality (generally owing to its association with coronary and carotid artery disease). PAD is responsible for approximately half a million hospitalizations and 100 000 angiograms annually.1,2 In part, because of a general unfamiliarity with these diseases among the primary care community, PAD patients receive suboptimal treatment in comparison with patients with coronary artery disease (CAD), being prescribed therapeutic doses of statins, antihypertensive medicines, and antiplatelet agents less commonly than patients with CAD.3–6 Much remains unknown about the biological origins of this disease and how to effectively identify and treat affected individuals. A greater understanding of how genetic variation influences susceptibility to PAD may inform the development of novel therapeutics. High-throughput, whole-genome technology efforts have recently made inroads toward these goals (Table). The advent …

Modeling Brain Disease in a Dish: Really?

Cellular programming and reprogramming technology (CPART) presents a novel approach for understanding disease progression and mechanism. In addition, CPART provides an innovative opportunity for developing diagnostic tools and novel drug candidates for therapy. In this Forum, we will discuss obstacles and solutions for modeling brain disease using CPART.

Advances in Whole-Genome Genetic Testing: From Chromosomes to Microarrays

Whole-genome genetic diagnostics has changed the clinical landscape of pediatric and adolescent medicine. In this article, we review the history of clinical cytogenetics as the field has progressed from studying chromosomes prepared from cells squashed between 2 slides to the high-resolution, whole-genome technology in use today, which has allowed for the identification of numerous previously unrecognized microdeletion and microduplication syndromes. Types of arrays and the data they collect are addressed, as are the types of results that array comparative genomic hybridization studies may generate. Throughout the review, we present case stories to illustrate the familiar (Down syndrome) and the new (a never-before reported microdeletion on the long arm of chromosome 12).

Addition of multiple rare SNPs to known common variants improves the association between disease and gene in the Genetic Analysis Workshop 17 data

The upcoming release of new whole-genome genotyping technologies will shed new light on whether there is an associative effect of previously immeasurable rare variants on incidence of disease. For Genetic Analysis Workshop 17, our team focused on a statistical method to detect associations between gene-based multiple rare variants and disease status. We added a combination of rare SNPs to a common variant shown to have an influence on disease status. This method provides us with an enhanced ability to detect the effect of these rare variants, which, modeled alone, would normally be undetectable. Adjusting for significant clinical parameters, several genes were found to have multiple rare variants that were significantly associated with disease outcome.

Gene-expression profiling in pancreatic cancer

Pancreatic cancer has one of the worst prognoses, owing principally to a late diagnosis and the absence of good treatments. In the last 5 years, up to 12 molecular pathways involved in pancreatic cancer have been described. Global gene-expression profiling and the use of microarray databases have allowed the identification of hundreds of genes that are differentially expressed in pancreatic cancer. However, validation of these genes as biomarkers for early diagnosis, prognosis or treatment efficacy is still incomplete. Additionally, microRNAs have emerged as a potential source of variation between cancer and normal samples, and several of them have been identified as being deregulated in pancreatic tumors. An integrative point of view in the study of pancreatic cancer that makes use of all the whole-genome technologies has revealed several molecular mechanisms that affect pancreatic cancer development. These results should encourage the use of more personalized medicine in this pathology. Recent developments and future perspectives are discussed.

Multiple sclerosis pharmacogenomics

Genetic polymorphisms and variable expression of drug receptors, metabolizing enzymes, and transporters have been linked to interindividual differences in efficacy and toxicity of many Food and Drug Administration-approved therapeutic agents. In multiple sclerosis, the combination of heterogeneity of disease pathology and significant variation in clinical response to disease-modifying agents necessitates the definition of biomarkers that can a priori predict therapeutic response and define appropriate therapeutic regimens. Pharmacogenomic studies will directly address the question of heterogeneity by analysis of the correlation between different genomic variants and clinical responses to therapy. These studies will include longitudinal designs, maximize clinical response variables, include whole-genome technologies, use large patient cohorts, and require the development of novel mathematical algorithms designed to integrate the wealth of disparate data to identify modest genetic effects and interactions.

Genetic overlap between autism, schizophrenia and bipolar disorder

There is strong evidence that genetic factors make substantial contributions to the etiology of autism, schizophrenia and bipolar disorders, with heritability estimates being at least 80% for each. These illnesses have complex inheritance, with multiple genetic and environmental factors influencing disease risk; however, in psychiatry, complex genetics is further compounded by phenotypic complexity. Autism, schizophrenia and bipolar disorder are effectively syndromic constellations of symptoms that define groups of patients with broadly similar outcomes and responses to treatment. As such the diagnostic categories are likely to be heterogeneous and the boundaries between them somewhat arbitrary. Recent applications of whole-genome technologies have discovered rare copy number variants and common single-nucleotide polymorphisms that are associated with risk of developing these disorders. Furthermore, these studies have shown an overlap between the genetic loci and even alleles that predispose to the different phenotypes. The findings have several implications. First, they show that copy number variations are likely to be important risk factors for autism and schizophrenia, whereas common single-nucleotide polymorphism alleles have a role in all disorders. Second, they imply that there are specific genetic loci and alleles that increase an individual's risk of developing any of these disorders. Finally, the findings suggest that some of the specific genetic loci implicated so far encode proteins, such as neurexins and neuroligins, that function in synaptic development and plasticity, and therefore may represent a common biological pathway for these disorders.