Emerging patent issues in genomic diagnostics.
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Genetic Testing↗
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A physician's guide to the human genome.
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Forecasting↗
[Trends in residual risk of transfusion-transmitted viral infections (HIV, HCV, HBV) in France between 1992 and 2002 and impact of viral genome screening (Nucleic Acid Testing)].
BACKGROUND: Monitoring trends in residual risk of transfusion-transmitted viral infections is important to assess improvements in blood safety. These trends were analysed over nine overlapping periods of 3 years from 1992 to 2002. The 2000-2002 estimates were compared to the results of HIV-1 and HCV NAT implemented on all blood donations in July 2001. METHOD: As risk is mainly associated with the window period, residual risks were estimated by multiplying incidence rates by the durations of the window periods. For the first seven periods, incidence rates were calculated from data collected by the blood centres belonging to the Transfusion-Transmissible Agents Working Group which collect more than 50% of blood donations in France, and for the two last periods, on the overall blood supply. RESULTS: On the 2000-2002 period, residual risks without NAT were estimated at 1 in 1,400,000 for HIV, at 1 in 1,000,000 for HCV and at 1 in 400,000 for HBV. With minipool NAT, the residual risk become nearly two times lower for HIV (1 in 2.5 million donations) and seven times lower for HCV (1 in 6.65 million donations). For HIV, of the 4.9 million donations screened with NAT between July 2001 and June 2003, two were remote thanks to the NAT, which is consistent with the NAT expected yield. Concerning HCV, one out of the four WP predicted cases was detected with NAT. Without NAT, the overall residual risk for the three viruses combined (HIV, HCV, HBV) decreased from 1 in 65,000 to 1 in 235,000 donations between 1992 and 2002. Since the implementation of NAT, the current overall residual risk is 1 in 325,000 donations (28% less than without NAT). CONCLUSION: NAT results confirm the validity of residual risk estimates given by the model, and the limited benefit of genomic screening due to the very low level of residual risk at the time of its implementation.
DNA, Viral↗
Testing of a whole genome PCR scanning approach to identify genomic variability in four different species of lactic acid bacteria.
Genomes can be markedly heterogeneous in conspecific bacterial strains. Genome sequences can be used to analyze genome plasticity via a PCR(2) (plasticity of chromosome revealed by PCR) approach. Small-sized chromosomes can indeed be fully amplified by long-range PCR with a set of primers designed using a reference strain and then applied to several other strains. Analysis of the resulting patterns can reveal genome plasticity. GenoFrag, a software package for the design of primers optimized for PCR(2) [N. Ben Zakour, M. Gautier, R. Andonov, D. Lavenier, M.F. Cochet, P. Veber, A. Sorokin, Y. Le Loir, GenoFrag: Software to design primers optimized for whole genome scanning by long-range PCR amplification, Nucleic Acids Res. 32 (2004) 17-24] was developed for the analysis of bacterial genome plasticity by whole genome amplification in approximately 10-kb-long fragments. By applying GenoFrag, we provide herewith evidence that genome plasticity can be analyzed in lactic acid bacteria using a PCR(2) approach. The genome sequences of Lactococcus lactis IL1403, Lactobacillus plantarum WCFS1, Lactobacillus bulgaricus ATCC11842 and Bifidobacterium longum NCC2705 were used to design four sets of primers. Each set was evaluated in silico to check that it ensured optimum coverage of the bacterial chromosome. To validate the primers generated by GenoFrag, a subset of primers was successfully used in LR-PCR experiments on genomic DNA from four L. bulgaricus strains.
Bacterial Typing Techniques↗
Structure-based assignment of the biochemical function of a hypothetical protein: a test case of structural genomics.
Many small bacterial, archaebacterial, and eukaryotic genomes have been sequenced, and the larger eukaryotic genomes are predicted to be completely sequenced within the next decade. In all genomes sequenced to date, a large portion of these organisms' predicted protein coding regions encode polypeptides of unknown biochemical, biophysical, and/or cellular functions. Three-dimensional structures of these proteins may suggest biochemical or biophysical functions. Here we report the crystal structure of one such protein, MJ0577, from a hyperthermophile, Methanococcus jannaschii, at 1.7-A resolution. The structure contains a bound ATP, suggesting MJ0577 is an ATPase or an ATP-mediated molecular switch, which we confirm by biochemical experiments. Furthermore, the structure reveals different ATP binding motifs that are shared among many homologous hypothetical proteins in this family. This result indicates that structure-based assignment of molecular function is a viable approach for the large-scale biochemical assignment of proteins and for discovering new motifs, a basic premise of structural genomics.
Adenosine Triphosphatases↗
The Centre for Modeling Human Disease Gene Trap resource.
Gene trap mutagenesis of mouse embryonic stem cells generates random loss-of-function mutations, which can be identified by a sequence tag and can often report the endogenous expression of the mutated gene. The Centre for Modeling Human Disease is performing expression- and sequence-based screens of gene trap insertions to generate new mouse mutations as a resource for the scientific community. The gene trap insertions are screened using multiplexed in vitro differentiation and induction assays, and sequence tags are generated to complement expression profiles. Researchers may search for insertions in genes expressed in target cell lineages, under specific in vitro conditions, or based upon sequence identity via an online searchable database (http://www.cmhd.ca/sub/genetrap.asp). The clones are available as a resource to researchers worldwide to help to functionally annotate the mammalian genome and will serve as a source to test candidate loci identified by phenotype-driven mutagenesis screens.
Animals↗
454 sequencing put to the test using the complex genome of barley.
BACKGROUND: During the past decade, Sanger sequencing has been used to completely sequence hundreds of microbial and a few higher eukaryote genomes. In recent years, a number of alternative technologies became available, among them adaptations of the pyrosequencing procedure (i.e. "454 sequencing"), promising an approximately 100-fold increase in throughput over Sanger technology--an advancement which is needed to make large and complex genomes more amenable to full genome sequencing at affordable costs. Although several studies have demonstrated its potential usefulness for sequencing small and compact microbial genomes, it was unclear how the new technology would perform in large and highly repetitive genomes such as those of wheat or barley. RESULTS: To study its performance in complex genomes, we used 454 technology to sequence four barley Bacterial Artificial Chromosome (BAC) clones and compared the results to those from ABI-Sanger sequencing. All gene containing regions were covered efficiently and at high quality with 454 sequencing whereas repetitive sequences were more problematic with 454 sequencing than with ABI-Sanger sequencing. 454 sequencing provided a much more even coverage of the BAC clones than ABI-Sanger sequencing, resulting in almost complete assembly of all genic sequences even at only 9 to 10-fold coverage. To obtain highly advanced working draft sequences for the BACs, we developed a strategy to assemble large parts of the BAC sequences by combining comparative genomics, detailed repeat analysis and use of low-quality reads from 454 sequencing. Additionally, we describe an approach of including small numbers of ABI-Sanger sequences to produce hybrid assemblies to partly compensate the short read length of 454 sequences. CONCLUSION: Our data indicate that 454 pyrosequencing allows rapid and cost-effective sequencing of the gene-containing portions of large and complex genomes and that its combination with ABI-Sanger sequencing and targeted sequence analysis can result in large regions of high-quality finished genomic sequences.
Base Pairing↗
[Diagnostic tests: Hepatitis C virus genome (HCV RNA)].
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Biomarkers↗
[Genetic, genomic and nucleic acid testing services provided by commercial laboratories].
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Clinical Laboratory Techniques↗
Paired Exome-Based Comprehensive Genomic Profiling and Germline Genetic Testing for Unselected Patients With Colorectal Cancer in a Multicenter Prospective Study.
BACKGROUND AND AIMS: Comprehensive genomic profiling (CGP) for tumors and germline genetic testing (GGT) inform precision therapy and clinical management of patients with colorectal cancer (CRC), and evidence is growing in support of universal paired CGP-GGT patient testing. However, the utility of combining CGP and GGT for early-stage CRC (ESC) and early-onset CRC (EOC) is unclear. METHODS: We performed a prospective, multisite study featuring GGT using an 80+ gene next-generation sequencing platform and exome-based CGP among CRC patients (unselected for age, stage, family history) receiving care at Mayo Clinic Cancer Centers between April 1, 2018, and March 31, 2020. RESULTS: A total of 150 CRC patients had GGT and exome-based CGP performed. ESC patients had an enrichment of high microsatellite instability and high tumor mutation burden. High microsatellite instability was also enriched in those with smoking history, and in tumors with mutated BRAF, homologous recombination deficiency, or at least 1 variant in the rat sarcoma virus pathway. Moreover, patients with smoking history were enriched in BRAF and other Tier 1 or 2 variants overall. Sixteen percent of patients harbored a pathogenic germline variant, most frequent being in Lynch syndrome genes. Paired GGT and CGP testing had high rates of clinically significant findings (≈70%) with the most frequent being high tumor mutation burden status. Pathway and mutational signature analysis revealed frequent CGP mutations in DNA repair and cell cycle pathways. CONCLUSION: These data suggest that universal, combined GGT-CGP increases clinical utility for EOC and ESC patients. This is key for EOC patients who tend to experience poorer outcomes. CGP-GGT expedites germline resolution for tumor mutations in hereditary cancer genes, reducing delays and facilitating identification of relevant therapies, clinical trials, and management recommendations.
Colorectal Cancer↗
Testing untyped alleles (TUNA)-applications to genome-wide association studies.
The large number of tests performed in analyzing data from genome-wide association studies has a large impact on the power of detecting risk variants, and analytic strategies specifying the optimal set of hypotheses to be tested are necessary. We propose a genome-wide strategy that is based on one degree of freedom tests for all the genotyped variants, and for all the untyped variants for which there is sufficient information in the observed data. The set of untyped variants to be tested is found using multi-locus measures of linkage disequilibrium and haplotype frequencies from a reference database such as HapMap (The International HapMap Consortium [2003] Nature 426:789-796). We introduce a novel statistic for testing differences in allele frequencies for untyped variation that is based on linear combinations of estimable haplotype frequencies. Algorithms for finding the sets of genotyped markers to be used in testing an untyped allele, and ways of incorporating haplotypes observed in the study data but not in the reference database are also described. The proposed testing strategy can be used as the first step in the analysis of genome-wide association data, and, because every performed test is directed to a marker, it can be used to specify the set of polymorphisms to genotype in follow-up studies. The described methodology provides also a tool for joint analysis of data from studies done on different platforms.
Algorithms↗
The future of genomics: hope or hype?
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Genetic Testing↗
Growth regulation in Peromyscus species hybrids: a test for mitochondrial-nuclear genomic interaction.
Interspecific hybridization of Peromyscus maniculatus (deer mouse) and P. polionotus (oldfield mouse) is accompanied by pronounced size differences between reciprocal F1 animals beginning in the fetus and continuing throughout life. Since the mitochondrial genome is inherited through the maternal line in Peromyscus, we tested the hypothesis that increased disparity between the species sources of mitochondrial and nuclear genomes within animals would exaggerate the reciprocal size effects through misregulation of growth, whereas species-compatible genomes were postulated to diminish the effect. Four series of backcrosses were established from females of the two reciprocal F1, while insuring continuity of the maternal mitochondrial composition at each generation. Size and weight measurements were made on neonatal, ten-day and six-month old animals through four or more backcross generations. Contrary to the hypothesis, deer mice with P. polionotus mitochondrial DNA, but 98% or more P. maniculatus nuclear composition, and animals with P. maniculatus mitochondria and principally P. polionotus nuclear genome regressed in mean size parameters to those of P. maniculatus and P. polionotus, respectively. Most of the regression was accounted for by the second backcross generation, and second and later backcross progeny did not differ significantly from the respective parental species controls. Maternal inheritance of mitochondrial DNA was confirmed by restriction enzyme analysis at the second and fifth backcross generation. Hybrid maternal effects in this Peromyscus cross are likely attributable to mechanisms other than nuclear-mitochondrial genomic interaction.
Animals↗
SINE retrotransposition during the evolution of the Pecoran ruminants.
SINE retrotransposition events have proven their value as phylogenetic markers in several eukaryotic taxa at different taxonomic levels. The genomes of ruminants contain three related SINE elements, Bov-tA, Bov-A2, and Bov-B. To estimate the time points of retrotransposition of individual copies of these SINEs, we designed PCR primers on database sequences containing SINE insertions in cattle, sheep, or goat genomes and tested for the presence of these copies in the genomes of other ruminants. It was checked by sequencing whether length variation of the PCR products reflected a SINE retrotransposition. One Bov-B and nine Bov-tA insertions were shared by cattle, sheep, goat, and giraffe, indicating an early retrotransposition event before the radiation of the Pecora, while three other Bov-tA and two Bov-B elements were apparently inserted later. The ruminant alpha-lactalbumine gene contains a hotspot of early and more recent Bov-tA insertions, a Bov-tA replacement as well as a recent Bov-B insertion. Three Bov-A2 insertions were found to be shared only by the Bovidae, the Bovini, and the Bos and Bison species, respectively, indicating that most Bov-A2 insertions are relatively recent. The time elapsed since the retrotransposition was also reflected in the degeneration of the direct repeats that flank SINE inserts. We suggest that retrotransposition of SINEs may serve as phylogenetic markers in the ruminant families, subfamilies, and even tribes. In addition, sequencing of SINE insertions revealed several other unique deletions/insertions that also may be informative for phylogenetic reconstructions of ruminants.
Animals↗
Horizontal transmission of the Leningrad-3 live attenuated mumps vaccine virus.
Here we describe symptomatic transmission of the Leningrad-3 mumps vaccine virus from healthy vaccinees to previously vaccinated contacts. Throat swab and serum samples were taken from six symptomatic mumps cases and from 13 family contacts. Assessment of serum IgG and IgM anti-mumps virus antibodies and IgG avidity testing was performed using commercial test kits. Sera neutralizing antibodies were measured by plaque reduction neutralization assay using the L-3 vaccine mumps virus as the target. All six of the symptomatic mumps cases and three contact subjects tested positive for mumps by RT-PCR. The genomic sequences tested (F, SH and HN genes) of all nine of these samples were identical to the L-3 mumps vaccine strain. All 13 contacts were asymptomatic; however clear serological evidence of mumps infection was found in some of them. The likely epidemiological source of the transmitted L-3 mumps virus was children who were recently vaccinated at the schools attended by the six symptomatic mumps patients described here. The L-3 mumps vaccine virus can be shed and transmitted horizontally, even to subjects previously vaccinated with the same virus.
Adolescent↗
Prader Willi and Angelman syndromes: exemplars of genomic imprinting.
The molecular phenomenon genomic imprinting provides an explanation for why two clinically distinct syndromes share genetic etiologies. Increased understanding of genomic imprinting is affecting diagnostics. Use of improved diagnostic tests can enable early, syndrome-specific, and anticipatory interventions and consequently, improved quality of life; however, these tests are of little use unless clinicians are able to identify at-risk patients. Nurses knowledgeable about Prader Willi and Angelman syndromes and their associated genetic mechanisms can play a significant role in early identification, referral, and intervention of patients with these conditions.
Angelman Syndrome↗
[Analysis of subtype of porcine endogenous retrovirus in two species of Chinese pigs].
OBJECTIVE: To analyze the subtype of porcine endogenous retrovirus (PERV) in two species of Chinese pigs-Wu zhishan pig and Banna minipig inbred; the total number of pigs being eighty six. METHODS: Three primers which are specific for the three PERV subtypes (subtypes A, B and C) were used to amplify the genome DNA extracted from the pigs. RESULTS: In all tested pigs' genome, subtype C was not found; in 77.9% pigs, double positive envAB were found; in 22.1% pigs, only A or B was found. CONCLUSION: In the genome of peripheral leukocytes from Wuzhishan pig and Banna minipig inbred, only subtypes A and B exist, and envAB predominate.
Animals↗