A feasibility study testing four hypotheses with phase II outcomes in advanced colorectal cancer (MRC FOCUS3): a model for randomised controlled trials in the era of personalised medicine?

BACKGROUND: Molecular characteristics of cancer vary between individuals. In future, most trials will require assessment of biomarkers to allocate patients into enriched populations in which targeted therapies are more likely to be effective. The MRC FOCUS3 trial is a feasibility study to assess key elements in the planning of such studies. PATIENTS AND METHODS: Patients with advanced colorectal cancer were registered from 24 centres between February 2010 and April 2011. With their consent, patients' tumour samples were analysed for KRAS/BRAF oncogene mutation status and topoisomerase 1 (topo-1) immunohistochemistry. Patients were then classified into one of four molecular strata; within each strata patients were randomised to one of two hypothesis-driven experimental therapies or a common control arm (FOLFIRI chemotherapy). A 4-stage suite of patient information sheets (PISs) was developed to avoid patient overload. RESULTS: A total of 332 patients were registered, 244 randomised. Among randomised patients, biomarker results were provided within 10 working days (w.d.) in 71%, 15 w.d. in 91% and 20 w.d. in 99%. DNA mutation analysis was 100% concordant between two laboratories. Over 90% of participants reported excellent understanding of all aspects of the trial. In this randomised phase II setting, omission of irinotecan in the low topo-1 group was associated with increased response rate and addition of cetuximab in the KRAS, BRAF wild-type cohort was associated with longer progression-free survival. CONCLUSIONS: Patient samples can be collected and analysed within workable time frames and with reproducible mutation results. Complex multi-arm designs are acceptable to patients with good PIS. Randomisation within each cohort provides outcome data that can inform clinical practice.

Diagnosis of copy number variation by Illumina next generation sequencing is comparable in performance to oligonucleotide array comparative genomic hybridisation.

Array comparative genomic hybridisation (aCGH) profiling is currently the gold standard for genetic diagnosis of copy number. Next generation sequencing technologies provide an alternative and adaptable method of detecting copy number by comparing the number of sequence reads in non-overlapping windows between patient and control samples. Detection of copy number using the BlueGnome 8×60k oligonucleotide aCGH platform was compared with low resolution next generation sequencing using the Illumina GAIIx on 39 patients with developmental delay and/or learning difficulties who were referred to the Leeds Clinical Cytogenetics Laboratory. Sensitivity and workflow of the two platforms were compared. Customised copy number algorithms assessed sequence counts and detected changes in copy number. Imbalances detected on both platforms were compared. Of the thirty-nine patients analysed, all eleven imbalances detected by array CGH and confirmed by FISH or Q-PCR were also detected by CNV-seq. In addition, CNV-seq reported one purported pathogenic copy number variant that was not detected by array CGH. Non-pathogenic, unconfirmed copy number calls were detected by both platforms; however few were concordant between the two. CNV-seq offers an alternative to array CGH for copy number analysis with resolution and future costs comparable to conventional array CGH platforms and with less stringent sample requirements.

Attitudes towards prenatal testing and termination of pregnancy in British Pakistani parents and relatives of children with recessive conditions in the UK.

OBJECTIVE: To compare British Pakistani parents' and their relatives' attitudes to prenatal testing (PND) and termination of pregnancy (TOP) for a range of conditions. METHOD: A total of 222 British Pakistani participants: 117 parents of children with a child with a genetic condition (52 fathers and 65 mothers) and 103 of their relatives (51 males and 52 females) completed a structured questionnaire about their attitudes toward PND and TOP for 30 different conditions. RESULTS: Parents were more accepting of PND (P < 0.001) and TOP (P < 0.001) than their relatives for most of the conditions. Male relatives were consistently least interested in PND and TOP, except for conditions at the serious end of the continuum, where over 90% would opt for PND for quadriplegia and anencephaly, and over 60% would opt for TOP for these conditions. CONCLUSION: The lower level of interest in PND and TOP in relatives, particularly men, may be due to lack of information disseminated by parents about their child's recessive inheritance and its implications for relatives, resulting in poor understanding of genetic risk. These findings highlight the need for the provision of proactive genetic counselling to raise awareness of genetic risk and facilitate informed reproductive decision-making in at-risk relatives.

The surface of Mars: there view from the viking 1 lander.

The first photographs ever returned from the surface of Mars were obtained by two facsimile cameras aboard the Viking 1 lander, including black-and-white and color, 0.12 degrees and 0.04 degrees resolution, and monoscopic and stereoscopic images. The surface, on the western slopes of Chtyse Planitia, is a boulder-strewn deeply reddish desert, with distant eminences-some of which may be the rims of impact craters-surmounted by a pink sky. Both impact and aeolian processes are evident. After dissipation of a small dust cloud stirred by the landing maneuvers, no subsequent signs of movement were detected on the landscape, and nothing has been observed that is indicative of macroscopic biology at this time and place.

The surface of Mars: the view from the viking 2 lander.

Viking 2 lander began imaging the surface of Mars at Utopia Planitia on 3 September 1976. The surface is a boulder-strewn reddish desert cut by troughs that probably form a polygonal network. A plateau can be seen to the east of the spacecraft, which for the most probable lander location is approximately the direction of a tongue of ejecta from the crater Mie. Boulders at the lander 2 site are generally more vesicular than those near lander i. Fines at both lander sites appear to be very fine-grained and to be bound in a duricrust. The pinkish color of the sky, similar to that observed at the lander I site, indicates suspension of surface material. However, the atmospheric optical depth is less than that at the lander I site. After dissipation of a cloud of dust stirred during landing, no changes other than those stemming from sampling activities have been detected in the landscape. No signs of large organisms are apparent at either landing site.

Isolation of the thymidylate synthetase gene (TMP1) by complementation in Saccharomyces cerevisiae.

The structural gene (TMP1) for yeast thymidylate synthetase (thymidylate synthase; EC 2.1.1.45) was isolated from a chimeric plasmid bank by genetic complementation in Saccharomyces cerevisiae. Retransformation of the dTMP auxotroph GY712 and a temperature-sensitive mutant (cdc21) with purified plasmid (pTL1) yielded Tmp+ transformants at high frequency. In addition, the plasmid was tested for the ability to complement a bacterial thyA mutant that lacks functional thymidylate synthetase. Although it was not possible to select Thy+ transformants directly, it was found that all pTL1 transformants were phenotypically Thy+ after several generations of growth in nonselective conditions. Thus, yeast thymidylate synthetase is biologically active in Escherichia coli. Thymidylate synthetase was assayed in yeast cell lysates by high-pressure liquid chromatography to monitor the conversion of [6-3H]dUMP to [6-3H]dTMP. In protein extracts from the thymidylate auxotroph (tmp1-6) enzymatic conversion of dUMP to dTMP was barely detectable. Lysates of pTL1 transformants of this strain, however, had thymidylate synthetase activity that was comparable to that of the wild-type strain.

The nucleotide sequence of the murine Hox-D3 (Hox-4.1) gene reveals extensive identity with the human protein.

We report the sequence of the murine Hox-D3 gene, formerly referred to as Hox-4, Hox-4.1 and Hox-4A. This gene is located on murine chromosome 2 in the Hox-D complex. The predicted Hox-D3 protein comprises 417 amino acids and displays 95% identity to the human protein. We have demonstrated that Hox-D3 is expressed in the skin, kidney and thymus, but not in lung, liver, spleen or stomach.

Induction of intrachromosomal recombination in yeast by inhibition of thymidylate biosynthesis.

The biosynthesis of thymidylate in the yeast Saccharomyces cerevisiae can be inhibited by antifolate drugs. We have found that antifolate treatment enhances the formation of leucine prototrophs in a haploid strain of yeast carrying, on the same chromosome, two different mutant leu2 alleles separated by Escherichia coli plasmid sequences. That this effect is a consequence of thymine nucleotide depletion was verified by the finding that provision of exogenous thymidylate eliminates the increased production of Leu+ colonies. DNA hybridization analysis revealed that recombination, including reciprocal exchange, gene conversion and unequal sister-chromatid crossing over, between the duplicated genes gave rise to the induced Leu+ segregants. Although gene conversion unaccompanied by crossing over was responsible for the major fraction of leucine prototrophs, events involving reciprocal exchange exhibited the largest increase in frequency. These data show that recombination is induced between directly repeated DNA sequences under conditions of thymine nucleotide depletion. In addition, the results of this and previous studies are consistent with the possibility that inhibition of thymidylate biosynthesis in yeast may create a metabolic condition that provokes all forms of mitotic recombination.

The polymerase chain reaction: from functional genomics to high-school practical classes.

After a decade of intensive use as an in vitro alternative to cloning DNA, PCR is now well established as the default method for DNA and RNA analysis. Recent developments have consolidated this position by the introduction of more robust formats, improvements in thermal cyclers and labelling and detection methods. The trend is towards increasing automation, although comparatively few diagnostic kits based on PCR are in wide use. At the same time the applications of PCR are being extended with modifications such as long, accurate PCR and arrayed oligonucleotides or expressed sequences.

The polymerase chain reaction: new variations on an old theme.

The polymerase chain reaction (PCR) is firmly established as the method of choice for DNA amplification, though alternative strategies, such as the ligase chain reaction, may also be employed. Despite the continued development of PCR applications for gene mapping and diagnostics, few revolutionary improvements have been made to the technique. The major exception is long-accurate PCR, which has increased the length of amplifiable DNA by an order of magnitude.

Overview of spaceflight immunology studies.

The effects of spaceflight and analogues of spaceflight are discussed here and in nine accompanying articles. In this summary we present spaceflight studies with human subjects, animal subjects, and cell cultures and we review ground-based systems used to model the observed effects of spaceflight on the immune system. Human paradigms include bed rest, academic or psychological stress, physical stress, hypobaric or high altitude stress, and confinement. Animal models include antiorthostatic and orthostatic suspension, hypobarism, and confinement. The ten manuscripts in this collection were selected to provide a summary that should give the reader an overview of the various activities of spaceflight immunology researchers throughout the history of space travel. This manuscript identifies the major contributors to the study of spaceflight immunology, explains what types of studies have been conducted, and how they have changed over the years. Also presented is a discussion of the unusual limitations associated with spaceflight research and the efforts to develop appropriate ground-based surrogate model systems. Specific details, data, and mechanistic speculations will be held to a minimum, because they will be discussed in depth in the other articles in the collection.

Immune changes during short-duration missions.

Spaceflight materially influences the immune mechanism of humans and animals. Effects resulting from missions of less than 1 month are examined. Effects from longer missions are discussed in the companion paper by Konstantinova et al. Most immunology studies have involved analyses of subjects and samples from subjects obtained after flight, with the data being compared with similar data obtained before flight. These studies have demonstrated that short-duration missions can result in a postflight depression in blast cell transformation, major changes in cytokine function, and alterations in the relative numbers of immune cell populations. In addition to these post- vs. preflight studies, some data have been produced in flight. However, these in vitro analyses have been less than satisfactory because of differences between in-flight and ground-control conditions. Recently, both the U.S. and Russian space programs have started collecting in-flight, in vivo, cell-mediated immunity data. These studies have confirmed that the human cell-mediated immune system is blunted during spaceflight.

In vivo testing confirms a blunting of the human cell-mediated immune mechanism during space flight.

The cell-mediated immune (CMI) mechanism was evaluated in 10 space shuttle astronauts by measuring their delayed-type hypersensitivity response to seven common recall antigens. The Multitest CMI test system was used to administer antigens of tetanus, diphtheria, Streptococcus, Proteus, old tuberculin, Candida, and Trichophyton to the forearm 46 h before nominal mission termination; readings were conducted 2 h after landing. The mean number of reactions was reduced from 4.5 preflight to 3.0 inflight, and the mean reaction score was reduced from 21.4 to 13.7 mm inflight. The data presented suggest that the CMI system is still being degraded by space flight conditions on day 4 and that between day 5 and day 10, the depression maximizes and the system begins to adjust to the new conditions. The relation of these in vivo findings to previously reported in vitro results is discussed.

A comparison of methods for gene dosage analysis in HMSN type 1.

A number of different approaches are used in diagnostic laboratories to detect the 1.5 Mb duplication at 17p11.2 seen in approximately 70% of patients with hereditary motor and sensory neuropathy type 1 (HMSN1). Here we compare the methods used in UK diagnostic laboratories to detect the duplication. Samples referred to participating centres for HMSN testing were collected, randomised, and distributed for testing. One hundred samples were examined using five different methods; each method was tested by two independent laboratories. Identical results were obtained from all laboratories for 44 samples. The remaining samples were classified as duplication positive or duplication negative on the basis of the same result by two or more methods. A total of 95 samples were classified by more than one method, two were withdrawn from the study as the same result was not obtained by two methods, and three are thought to have a duplication smaller than 1.5 Mb. Seven of 49 duplications were not detected by methods used to detect the common junction fragment and the use of microsatellites failed to yield a result in four of 95 samples. Sequence tagged site (STS) dosage analysis was found to be the most sensitive of the methods tested, although this method was found to be the most likely to require repeat analysis. Eight samples gave discordant results between the two laboratories testing by the same method. Upon retesting, reasons for the initial incorrect result included processing and typographical errors.

Genetic analysis of the connexin-26 M34T variant: identification of genotype M34T/M34T segregating with mild-moderate non-syndromic sensorineural hearing loss.

Mutations in the human gap junction beta-2 gene (GJB2) that encodes connexin-26 have been shown to cause non-syndromic sensorineural hearing loss (NSSNHL) at the DFNB1 locus on 13q11. Functional and genetic data regarding the disease causing potential of one particular GJB2 sequence variant, 101 T-->C (M34T), have proven contradictory. In this study, we found the prevalence of the M34T allele in a cohort of white sib pairs and sporadic cases with NSSNHL from the United Kingdom and Ireland to be 3.179% of chromosomes screened. Significantly, we identified the first M34T/M34T genotype cosegregating in a single family with mid to high frequency NSSNHL. Screening a control population of 630 subjects we identified 25 M34T heterozygotes; however, no M34T homozygotes were detected. Surprisingly, the majority of M34T alleles (88%) were in cis with a 10 bp deletion in the 5' non-coding sequence. This non-coding deletion was also homozygous in the homozygous M34T subjects. Microsatellite analysis of flanking loci in M34T heterozygotes and controls does not define an extensive ancestral haplotype but preliminary data suggest two common alleles in subjects with the M34T allele. In summary, we provide data that support M34T acting as a recessive GJB2 allele associated with mild-moderate prelingual hearing impairment.

A common founder for the 35delG GJB2 gene mutation in connexin 26 hearing impairment.

Fifty to eighty percent of autosomal recessive congenital severe to profound hearing impairment result from mutations in a single gene, GJB2, that encodes the protein connexin 26. One mutation of this gene, the 35delG allele, is particularly common in white populations. We report evidence that the high frequency of this allelic variant is the result of a founder effect rather than a mutational hot spot in GJB2, which was the prevailing hypothesis. Patients homozygous for the 35delG mutation and normal hearing controls originating from Belgium, the UK, and the USA were genotyped for different single nucleotide polymorphisms (SNPs). Four SNPs mapped in the immediate vicinity of GJB2, while two were positioned up to 76 kb from it. Significant differences between the genotypes of patients and controls for the five SNPs closest to GJB2 were found, with nearly complete association of one SNP allele with the 35delG mutation. For the most remote SNP, we could not detect any association. We conclude that the 35delG mutation is derived from a common, albeit ancient founder.

Complex pediatric elbow injury: an uncommon case.

BACKGROUND: There is paucity of literature describing complex elbow trauma in the pediatric population. We described a case of an uncommon pediatric elbow injury comprised of lateral condyle fracture associated with posterolateral dislocation of elbow. CASE PRESENTATION: A 12-year-old boy sustained a direct elbow trauma and presented with Milch type II lateral condyle fracture associated with posterolateral dislocation of elbow. Elbow dislocation was managed by closed reduction. The elbow stability was assessed under general anaesthesia, followed by open K-wiring for the lateral condylar fracture fixation. The patient had an uneventful recovery with an excellent outcome at 39 months follow-up. CONCLUSION: Complex pediatric elbow injuries are quite unusual to encounter, the management of such fractures can be technically demanding. Concomitant elbow dislocation should be managed by closed reduction followed by open reduction and internal fixation (K-wires or cannulated screws) of the lateral condyle fracture.

The detection of large deletions or duplications in genomic DNA.

While methods for the detection of point mutations and small insertions or deletions in genomic DNA are well established, the detection of larger (>100 bp) genomic duplications or deletions can be more difficult. Most mutation scanning methods use PCR as a first step, but the subsequent analyses are usually qualitative rather than quantitative. Gene dosage methods based on PCR need to be quantitative (i.e., they should report molar quantities of starting material) or semi-quantitative (i.e., they should report gene dosage relative to an internal standard). Without some sort of quantitation, heterozygous deletions and duplications may be overlooked and therefore be under-ascertained. Gene dosage methods provide the additional benefit of reporting allele drop-out in the PCR. This could impact on SNP surveys, where large-scale genotyping may miss null alleles. Here we review recent developments in techniques for the detection of this type of mutation and compare their relative strengths and weaknesses. We emphasize that comprehensive mutation analysis should include scanning for large insertions and deletions and duplications.

Genomic deletions in MSH2 or MLH1 are a frequent cause of hereditary non-polyposis colorectal cancer: identification of novel and recurrent deletions by MLPA.

Gene dosage abnormalities account for a significant proportion of the mutations in genes tested in DNA diagnostic laboratories. Detection of these changes has proved a challenge as the methods available to date are time consuming or unreliable. The multiplex ligation-dependent probe assay (MLPA) is a new technique allowing relative quantification of up to 40 different nucleic acid sequences in a single reaction tube. We have evaluated MLPA for potential use in the diagnostic setting against the following criteria: accuracy, reagent cost, hands-on time, reliability, and retests required. A total of 215 UK patients referred for genetic testing on the basis of a family history consistent with autosomal dominant hereditary non-polyposis colorectal cancer (HNPCC or Lynch syndrome) were tested by MLPA. Of these, 12 cases with deletions of one or more exons were identified, six with MLH1 deletions and six with MSH2 deletions. Test failure rates were less than 5% and overall mutation detection sensitivity in this series was increased by approximately 50% by the inclusion of MLPA for an additional testing cost of about 10%. Two novel mutations in MSH2 and 10 novel point mutations in MLH1 were also identified during the course of this study. We conclude that MLPA is a cost effective and robust gene dosage method that can be readily adopted by diagnostic services. Comprehensive mutation scanning for MSH2 and MLH1 is incomplete without gene dosage analysis.

Search for cytomegalovirus in postmortem brain tissue from patients with Huntington's chorea and other psychiatric disease by molecular hybridization using cloned DNA.

Postmortem human brain extracts were examined for the presence of human cytomegalovirus (CMV) DNA by molecular hybridization using a dot blot technique. The method was able to detect picogram quantities of homologous DNA, but CMV specific hybridization was detected in only one of 83 brains examined. The positive case came from a patient who had received immunosuppressive therapy. We were not able to confirm the report that CMV is present in the brains of patients with Huntington's chorea, nor was CMV detected in the temporal cortex of brains from schizophrenic patients. Our findings are discussed in relation to the methodology for investigating a possible viral etiology of some neuropsychiatric diseases.