Insights for precision oncology from the integration of genomic and clinical data of 13,880 tumors from the 100,000 Genomes Cancer Programme

The Cancer Programme of the 100,000 Genomes Project was an initiative to provide whole-genome sequencing (WGS) for patients with cancer, evaluating opportunities for precision cancer care within the UK National Healthcare System (NHS). Genomics England, alongside NHS England, analyzed WGS data from 13,880 solid tumors spanning 33 cancer types, integrating genomic data with real-world treatment and outcome data, within a secure Research Environment. Incidence of somatic mutations in genes recommended for standard-of-care testing varied across cancer types. For instance, in glioblastoma multiforme, small variants were present in 94% of cases and copy number aberrations in at least one gene in 58% of cases, while sarcoma demonstrated the highest occurrence of actionable structural variants (13%). Homologous recombination deficiency was identified in 40% of high-grade serous ovarian cancer cases with 30% linked to pathogenic germline variants, highlighting the value of combined somatic and germline analysis. The linkage of WGS and longitudinal life course clinical data allowed the assessment of treatment outcomes for patients stratified according to pangenomic markers. Our findings demonstrate the utility of linking genomic and real-world clinical data to enable survival analysis to identify cancer genes that affect prognosis and advance our understanding of how cancer genomics impacts patient outcomes.

Whole genome sequencing refines stratification and therapy of patients with clear cell renal cell carcinoma

Clear cell renal cell carcinoma (ccRCC) is the most common form of kidney cancer, but a comprehensive description of its genomic landscape is lacking. We report the whole genome sequencing of 778 ccRCC patients enrolled in the 100,000 Genomes Project, providing the most detailed somatic mutational landscape to date. We identify new driver genes, which as well as emphasising the major role of epigenetic regulation in ccRCC highlight additional biological pathways extending opportunities for drug repurposing. Genomic characterisation identified patients with divergent clinical outcome; higher number of structural copy number alterations associated with poorer prognosis, whereas VHL mutations were independently associated with a better prognosis. The twin observations that higher T-cell infiltration is associated with better outcome and that genetically predicted immune evasion is not common supports the rationale for immunotherapy. These findings should inform personalised surveillance and treatment strategies for ccRCC patients.

Whole-genome sequencing of chronic lymphocytic leukemia identifies subgroups with distinct biological and clinical features

The value of genome-wide over targeted driver analyses for predicting clinical outcomes of cancer patients is debated. Here, we report the whole-genome sequencing of 485 chronic lymphocytic leukemia patients enrolled in clinical trials as part of the United Kingdom's 100,000 Genomes Project. We identify an extended catalog of recurrent coding and noncoding genetic mutations that represents a source for future studies and provide the most complete high-resolution map of structural variants, copy number changes and global genome features including telomere length, mutational signatures and genomic complexity. We demonstrate the relationship of these features with clinical outcome and show that integration of 186 distinct recurrent genomic alterations defines five genomic subgroups that associate with response to therapy, refining conventional outcome prediction. While requiring independent validation, our findings highlight the potential of whole-genome sequencing to inform future risk stratification in chronic lymphocytic leukemia.

Frequency of pathogenic germline variants in cancer susceptibility genes in 1336 renal cell carcinoma cases

Renal cell carcinoma (RCC) occurs in a number of cancer predisposition syndromes, but the genetic architecture of susceptibility to RCC is not well defined. We investigated the frequency of pathogenic and likely pathogenic (P/LP) germline variants in cancer susceptibility genes (CSGs) within a large series of unselected RCC participants. Whole-genome sequencing data on 1336 RCC participants and 5834 controls recruited to the UK 100 000 Genomes Project, a nationwide multicentre study, was analyzed to identify rare P/LP short variants (single nucleotide variants and insertions/deletions ranging from 1 to 50 base pairs) and structural variants in 121 CSGs. Among 1336 RCC participants [mean: 61.3 years (±12 SD), range: 13-88 years; 64% male], 85 participants [6.4%; 95% CI (5.1, 7.8)] had one or more P/LP germline variant in a wider range of CSGs than previously recognized. A further 64 intragenic variants in CSGs previously associated with RCC were classified as a variant of uncertain significance (VUS) (24 'hot VUSs') and were considered to be of potential clinical relevance as further evaluation might results in their reclassification. Most patients with P variants in well-established CSGs known to predispose to renal cell carcinoma (RCC-CSGs) were aged <50 years. Burden test analysis for filtered variants in CSGs demonstrated a significant excess of CHEK2 variants in European RCC participants compared with the healthy European controls (P = 0.0019). Approximately, 6% of the patients with RCC unselected for family history have a germline variant requiring additional follow-up analysis. To improve diagnostic yield, we suggest expanding the panel of RCC-CSGs tested to include CHEK2 and all SDHx subunits and raising the eligibility criteria for age-based testing.

Germline MBD4 deficiency causes a multi-tumor predisposition syndrome

We report an autosomal recessive, multi-organ tumor predisposition syndrome, caused by bi-allelic loss-of-function germline variants in the base excision repair (BER) gene MBD4. We identified five individuals with bi-allelic MBD4 variants within four families and these individuals had a personal and/or family history of adenomatous colorectal polyposis, acute myeloid leukemia, and uveal melanoma. MBD4 encodes a glycosylase involved in repair of G:T mismatches resulting from deamination of 5'-methylcytosine. The colorectal adenomas from MBD4-deficient individuals showed a mutator phenotype attributable to mutational signature SBS1, consistent with the function of MBD4. MBD4-deficient polyps harbored somatic mutations in similar driver genes to sporadic colorectal tumors, although AMER1 mutations were more common and KRAS mutations less frequent. Our findings expand the role of BER deficiencies in tumor predisposition. Inclusion of MBD4 in genetic testing for polyposis and multi-tumor phenotypes is warranted to improve disease management.

An enhanced genetic model of relapsed IGH-translocated multiple myeloma evolutionary dynamics

Most patients with multiple myeloma (MM) die from progressive disease after relapse. To advance our understanding of MM evolution mechanisms, we performed whole-genome sequencing of 80 IGH-translocated tumour-normal newly diagnosed pairs and 24 matched relapsed tumours from the Myeloma XI trial. We identify multiple events as potentially important for survival and therapy-resistance at relapse including driver point mutations (e.g., TET2), translocations (MAP3K14), lengthened telomeres, and increased genomic instability (e.g., 17p deletions). Despite heterogeneous mutational processes contributing to relapsed mutations across MM subtypes, increased AID/APOBEC activity is particularly associated with shorter progression time to relapse, and contributes to higher mutational burden at relapse. In addition, we identify three enhanced major clonal evolution patterns of MM relapse, independent of treatment strategies and molecular karyotypes, questioning the viability of "evolutionary herding" approach in treating drug-resistant MM. Our data show that MM relapse is associated with acquisition of new mutations and clonal selection, and suggest APOBEC enzymes among potential targets for therapy-resistant MM.

Germline-focussed analysis of tumour-only sequencing: recommendations from the ESMO Precision Medicine Working Group

It is increasingly common in oncology practice to perform tumour sequencing using large cancer panels. For pathogenic sequence variants in cancer susceptibility genes identified on tumour-only sequencing, it is often unclear whether they are of somatic or constitutional (germline) origin. There is wide-spread disparity regarding both the extent to which systematic 'germline-focussed analysis' is carried out upon tumour sequencing data and for which variants follow-up analysis of a germline sample is carried out. Here we present analyses of paired sequencing data from 17 152 cancer samples, in which 1494 pathogenic sequence variants were identified across 65 cancer susceptibility genes. From these analyses, the European Society of Medical Oncology Precision Medicine Working Group Germline Subgroup has generated (i) recommendations regarding germline-focussed analyses of tumour-only sequencing data, (ii) indications for germline follow-up testing and (iii) guidance on patient information-giving and consent.

p.Val804Met, the Most Frequent Pathogenic Mutation in RET, Confers a Very Low Lifetime Risk of Medullary Thyroid Cancer

CONTEXT

To date, penetrance figures for medullary thyroid cancer (MTC) for variants in rearranged during transfection (RET) have been estimated from families ascertained because of the presence of MTC.

OBJECTIVE

To gain estimates of penetrance, unbiased by ascertainment, we analyzed 61 RET mutations assigned as disease causing by the American Thyroid Association (ATA) in population whole-exome sequencing data.

DESIGN

For the 61 RET mutations, we used analyses of the observed allele frequencies in ∼51,000 individuals from the Exome Aggregation Consortium (ExAC) database that were not contributed via The Cancer Genome Atlas (TCGA; non-TCGA ExAC), assuming lifetime penetrance for MTC of 90%, 50%, and unbounded.

SETTING

Population-based.

RESULTS

Ten of 61 ATA disease-causing RET mutations were present in the non-TCGA ExAC population with observed frequency consistent with penetrance for MTC of >90%. For p.Val804Met, the lifetime penetrance for MTC, estimated from the allele frequency observed, was 4% [95% confidence interval (CI), 0.9% to 8%].

CONCLUSIONS

Based on penetrance analysis in carrier relatives of p.Val804Met-positive cases of MTC, p.Val804Met is currently understood to have high-lifetime penetrance for MTC (87% by age 70), albeit of later onset of MTC than other RET mutations. Given our unbiased estimate of penetrance for RET p.Val804Met of 4% (95% CI, 0.9% to 8%), the current recommendation by the ATA of prophylactic thyroidectomy as standard for all RET mutation carriers is likely inappropriate.

Promoter capture Hi-C-based identification of recurrent noncoding mutations in colorectal cancer

Efforts are being directed to systematically analyze the non-coding regions of the genome for cancer-driving mutations^1-6. cis-regulatory elements (CREs) represent a highly enriched subset of the non-coding regions of the genome in which to search for such mutations. Here we use high-throughput chromosome conformation capture techniques (Hi-C) for 19,023 promoter fragments to catalog the regulatory landscape of colorectal cancer in cell lines, mapping CREs and integrating these with whole-genome sequence and expression data from The Cancer Genome Atlas^7,8. We identify a recurrently mutated CRE interacting with the ETV1 promoter affecting gene expression. ETV1 expression influences cell viability and is associated with patient survival. We further refine our understanding of the regulatory effects of copy-number variations, showing that RASL11A is targeted by a previously identified enhancer amplification¹. This study reveals new insights into the complex genetic alterations driving tumor development, providing a paradigm for employing chromosome conformation capture to decipher non-coding CREs relevant to cancer biology.

Whole-genome sequencing of multiple myeloma reveals oncogenic pathways are targeted somatically through multiple mechanisms

Multiple myeloma (MM) is a biologically heterogeneous malignancy, however, the mechanisms underlying this complexity are incompletely understood. We report an analysis of the whole-genome sequencing of 765 MM patients from CoMMpass. By employing promoter capture Hi-C in naïve B-cells, we identify cis-regulatory elements (CREs) that represent a highly enriched subset of the non-coding genome in which to search for driver mutations. We identify regulatory regions whose mutation significantly alters the expression of genes as candidate non-coding drivers, including copy number variation (CNV) at CREs of MYC and single-nucleotide variants (SNVs) in a PAX5 enhancer. To better inform the interplay between non-coding driver mutations with other driver mechanisms, and their respective roles in oncogenic pathways, we extended our analysis identifying coding drivers in 40 genes, including 11 novel candidates. We demonstrate the same pathways can be targeted by coding and non-coding mutations; exemplified by IRF4 and PRDM1, along with BCL6 and PAX5, genes that are central to plasma cell differentiation. This study reveals new insights into the complex genetic alterations driving MM development and an enhanced understanding of oncogenic pathways.

Validation of Recently Proposed Colorectal Cancer Susceptibility Gene Variants in an Analysis of Families and Patients-a Systematic Review

High-throughput sequencing analysis has accelerated searches for genes associated with risk for colorectal cancer (CRC); germline mutations in NTHL1, RPS20, FANCM, FAN1, TP53, BUB1, BUB3, LRP6, and PTPN12 have been recently proposed to increase CRC risk. We attempted to validate the association between variants in these genes and development of CRC in a systematic review of 11 publications, using sequence data from 863 familial CRC cases and 1604 individuals without CRC (controls). All cases were diagnosed at an age of 55 years or younger and did not carry mutations in an established CRC predisposition gene. We found sufficient evidence for NTHL1 to be considered a CRC predisposition gene-members of 3 unrelated Dutch families were homozygous for inactivating p.Gln90Ter mutations; a Canadian woman with polyposis, CRC, and multiple tumors was reported to be heterozygous for the inactivating NTHL1 p.Gln90Ter/c.709+1G>A mutations; and a man with polyposis was reported to carry p.Gln90Ter/p.Gln287Ter; whereas no inactivating homozygous or compound heterozygous mutations were detected in controls. Variants that disrupted RPS20 were detected in a Finnish family with early-onset CRC (p.Val50SerfsTer23), a 39-year old individual with metachronous CRC (p.Leu61GlufsTer11 mutation), and a 41-year-old individual with CRC (missense p.Val54Leu), but not in controls. We therefore found published evidence to support the association between variants in NTHL1 and RPS20 with CRC, but not of other recently reported CRC susceptibility variants. We urge the research community to adopt rigorous statistical and biological approaches coupled with independent replication before making claims of pathogenicity.

CanVar: A resource for sharing germline variation in cancer patients

The advent of high-throughput sequencing has accelerated our ability to discover genes predisposing to disease and is transforming clinical genomic sequencing. In both contexts knowledge of the spectrum and frequency of genetic variation in the general population and in disease cohorts is vital to the interpretation of sequencing data. While population level data is becoming increasingly available from publicly accessible sources, as exemplified by The Exome Aggregation Consortium (ExAC), the availability of large-scale disease-specific frequency information is limited. These data are of particular importance to contextualise findings from clinical mutation screens and small gene discovery projects. This is especially true for cancer, which is typified by a number of hereditary predisposition syndromes.  Although mutation frequencies in tumours are available from resources such as Cosmic and The Cancer Genome Atlas, a similar facility for germline variation is lacking. Here we present the Cancer Variation Resource (CanVar) an online database which has been developed using the ExAC framework to provide open access to germline variant frequency data from the sequenced exomes of cancer patients. In its first release, CanVar catalogues the exomes of 1,006 familial early-onset colorectal cancer (CRC) patients sequenced at The Institute of Cancer Research. It is anticipated that CanVar will host data for additional cancers, providing a resource for others studying cancer predisposition and an example of how the research community can utilise the ExAC framework to share sequencing data.

Undefined familial colorectal cancer and the role of pleiotropism in cancer susceptibility genes

Although family history is a major risk factor for colorectal cancer (CRC) a genetic diagnosis cannot be obtained in over 50 % of familial cases when screened for known CRC cancer susceptibility genes. The genetics of undefined-familial CRC is complex and recent studies have implied additional clinically actionable mutations for CRC in susceptibility genes for other cancers. To clarify the contribution of non-CRC susceptibility genes to undefined-familial CRC we conducted a mutational screen of 114 cancer susceptibility genes in 847 patients with early-onset undefined-familial CRC and 1609 controls by analysing high-coverage exome sequencing data. We implemented American College of Medical Genetics and Genomics standards and guidelines for assigning pathogenicity to variants. Globally across all 114 cancer susceptibility genes no statistically significant enrichment of likely pathogenic variants was shown (6.7 % cases 57/847, 5.3 % controls 85/1609; P = 0.15). Moreover there was no significant enrichment of mutations in genes such as TP53 or BRCA2 which have been proposed for clinical testing in CRC. In conclusion, while we identified genes that may be considered interesting candidates as determinants of CRC risk warranting further research, there is currently scant evidence to support a role for genes other than those responsible for established CRC syndromes in the clinical management of familial CRC.

Rare disruptive mutations and their contribution to the heritable risk of colorectal cancer

Colorectal cancer (CRC) displays a complex pattern of inheritance. It is postulated that much of the missing heritability of CRC is enshrined in high-impact rare alleles, which are mechanistically and clinically important. In this study, we assay the impact of rare germline mutations on CRC, analysing high-coverage exome sequencing data on 1,006 early-onset familial CRC cases and 1,609 healthy controls, with additional sequencing and array data on up to 5,552 cases and 6,792 controls. We identify highly penetrant rare mutations in 16% of familial CRC. Although the majority of these reside in known genes, we identify POT1, POLE2 and MRE11 as candidate CRC genes. We did not identify any coding low-frequency alleles (1-5%) with moderate effect. Our study clarifies the genetic architecture of CRC and probably discounts the existence of further major high-penetrance susceptibility genes, which individually account for >1% of the familial risk. Our results inform future study design and provide a resource for contextualizing the impact of new CRC genes.

Torsion of Fatty Appendage of Falciform Ligament: Acute Abdomen in a Child

Torsion of the fatty appendage of the falciform ligament is an extremely rare condition that leads to severe abdominal pain and raised inflammatory markers. It can be recognised on ultrasound or CT scan. The pathophysiology is the same as that involved in the more common torsion and/or infarction of the greater omentum or epiploic appendages. The condition is best managed conservatively with anti-inflammatory analgesia, and the early recognition of this type of torsion may prevent unnecessary operative intervention to look for a source of abdominal pain. There have been five reported adult cases of a torted fatty appendage of the falciform ligament identified on ultrasound and CT scan, but no paediatric cases. We report a case of torsion of the fatty appendage of the falciform ligament in a ten-year-old boy and describe its imaging characteristics on CT scan.

TCF12 is mutated in anaplastic oligodendroglioma

Anaplastic oligodendroglioma (AO) are rare primary brain tumours that are generally incurable, with heterogeneous prognosis and few treatment targets identified. Most oligodendrogliomas have chromosomes 1p/19q co-deletion and an IDH mutation. Here we analysed 51 AO by whole-exome sequencing, identifying previously reported frequent somatic mutations in CIC and FUBP1. We also identified recurrent mutations in TCF12 and in an additional series of 83 AO. Overall, 7.5% of AO are mutated for TCF12, which encodes an oligodendrocyte-related transcription factor. Eighty percent of TCF12 mutations identified were in either the bHLH domain, which is important for TCF12 function as a transcription factor, or were frameshift mutations leading to TCF12 truncated for this domain. We show that these mutations compromise TCF12 transcriptional activity and are associated with a more aggressive tumour type. Our analysis provides further insights into the unique and shared pathways driving AO.

Genetic diagnosis of high-penetrance susceptibility for colorectal cancer (CRC) is achievable for a high proportion of familial CRC by exome sequencing

PURPOSE

Knowledge of the contribution of high-penetrance susceptibility to familial colorectal cancer (CRC) is relevant to the counseling, treatment, and surveillance of CRC patients and families.

PATIENTS AND METHODS

To quantify the impact of germline mutation to familial CRC, we sequenced the mismatch repair genes (MMR) APC, MUTYH, and SMAD4/BMPR1A in 626 early-onset familial CRC cases ascertained through a population-based United Kingdom national registry. In addition, we evaluated the contribution of mutations in the exonuclease domain (exodom) of POLE and POLD1 genes that have recently been reported to confer CRC risk.

RESULTS

Overall mutations (pathogenic, likely pathogenic) in MMR genes make the highest contribution to familial CRC (10.9%). Mutations in the other established CRC genes account for 3.3% of cases. POLE/POLD1 exodom mutations were identified in three patients with family histories consistent with dominant transmission of CRC. Collectively, mutations in the known genes account for 14.2% of familial CRC (89 of 626 cases; 95% CI = 11.5, 17.2).

CONCLUSION

A genetic diagnosis is feasible in a high proportion of familial CRC. Mainstreaming such analysis in clinical practice should enable the medical management of patients and their families to be optimized. Findings suggest CRC screening of POLE and POLD1 mutation carriers should be comparable to that afforded to those at risk of HNPCC. Although the risk of CRC associated with unexplained familial CRC is in general moderate, in some families the risk is substantive and likely to be the consequence of unidentified genes, as exemplified by POLE and POLD1. Our findings have utility in the design of genetic analyses to identify such novel CRC risk genes.

Rare variants of large effect in BRCA2 and CHEK2 affect risk of lung cancer

We conducted imputation to the 1000 Genomes Project of four genome-wide association studies of lung cancer in populations of European ancestry (11,348 cases and 15,861 controls) and genotyped an additional 10,246 cases and 38,295 controls for follow-up. We identified large-effect genome-wide associations for squamous lung cancer with the rare variants BRCA2 p.Lys3326X (rs11571833, odds ratio (OR) = 2.47, P = 4.74 × 10(-20)) and CHEK2 p.Ile157Thr (rs17879961, OR = 0.38, P = 1.27 × 10(-13)). We also showed an association between common variation at 3q28 (TP63, rs13314271, OR = 1.13, P = 7.22 × 10(-10)) and lung adenocarcinoma that had been previously reported only in Asians. These findings provide further evidence for inherited genetic susceptibility to lung cancer and its biological basis. Additionally, our analysis demonstrates that imputation can identify rare disease-causing variants with substantive effects on cancer risk from preexisting genome-wide association study data.

The silent mutational landscape of infant MLL-AF4 pro-B acute lymphoblastic leukemia

Over 90% of infants (< 1-year-old) diagnosed with leukemia have pro-B acute lymphoblastic leukemia (ALL) containing the MLL-AF4 fusion. When compared with other forms of paediatric ALL affecting later B-cell differentiation, MLL-AF4 pro-B is associated with a dismal prognosis with a typical 5-year disease-free survival of <20%. MLL-AF4 may be sufficient on its own for leukemogenesis or the gene-fusion product may alternatively predispose transformed cells to global genetic instability, enhancing the acquisition of additional key mutations. To gain insight into the genomic landscape of infant MLL-AF4 pro-B ALL we performed whole genome sequencing of diagnostic leukemic blasts and matched germline samples from three MLL-AF4 pro-B ALL infants. Our analysis revealed few somatic changes (copy number abnormalities, loss of heterozygosity, or single nucleotide variants), demonstrating that only a very small number of mutations are necessary to generate infant MLL-leukemia.

Germline mutations affecting the proofreading domains of POLE and POLD1 predispose to colorectal adenomas and carcinomas

Many individuals with multiple or large colorectal adenomas or early-onset colorectal cancer (CRC) have no detectable germline mutations in the known cancer predisposition genes. Using whole-genome sequencing, supplemented by linkage and association analysis, we identified specific heterozygous POLE or POLD1 germline variants in several multiple-adenoma and/or CRC cases but in no controls. The variants associated with susceptibility, POLE p.Leu424Val and POLD1 p.Ser478Asn, have high penetrance, and POLD1 mutation was also associated with endometrial cancer predisposition. The mutations map to equivalent sites in the proofreading (exonuclease) domain of DNA polymerases ɛ and δ and are predicted to cause a defect in the correction of mispaired bases inserted during DNA replication. In agreement with this prediction, the tumors from mutation carriers were microsatellite stable but tended to acquire base substitution mutations, as confirmed by yeast functional assays. Further analysis of published data showed that the recently described group of hypermutant, microsatellite-stable CRCs is likely to be caused by somatic POLE mutations affecting the exonuclease domain.

Technology-assisted and sutureless microvascular anastomoses: evidence for current techniques

BACKGROUND

Since the birth of reconstructive microvascular surgery, attempts have been made to shorten the operative time while maintaining patency and efficacy. Several devices have been developed to aid microsurgical anastomoses. This article investigates each of the currently available technologies and attempts to provide objective evidence supporting their use.

METHODS

Techniques of microvascular anastomosis were investigated by performing searches of the online databases Medline and Pubmed. Returned results were assessed according to the criteria for ranking medical evidence advocated by the Oxford Centre for Evidence Based Medicine. Emphasis was placed on publications with quantifiable endpoints such as unplanned return to theatre, flap salvage, and complication rates.

RESULTS

There is a relative paucity of high-level evidence supporting any form of assisted microvascular anastomosis. Specifically, there are no randomized prospective trials comparing outcomes using one method versus any other. However, comparative retrospective cohort studies do exist and have demonstrated convincing advantages of certain techniques. In particular, the Unilink™/3M™ coupler and the Autosuture™ Vessel Closure System® (VCS®) clip applicator have been shown to have level 2b evidence supporting their use, meaning that the body of evidence achieves a level of comparative cohort studies.

CONCLUSION

Of the available forms of assisted microvascular anastomoses, there is level 2b evidence suggesting a positive outcome with the use of the Unilink™/3M™ coupler and the Autosuture™ VCS® clip applicator. Other techniques such as cyanoacrylates, fibrin glues, the Medtronic™ U-Clip®, and laser bonding have low levels of evidence supporting their use. Further research is required to establish any role for these techniques.

Computed tomographic angiography: clinical applications

There has been a move towards increasingly refined techniques for autologous breast reconstruction, and given the substantial inter-individual variability of perforator anatomy, the need for reliable, accurate methods of vascular imaging has been sought. Computed tomographic angiography (CTA) can offer a range of applications in autologous breast reconstruction to aid surgical planning and improved outcomes. This article explores the utility of CTA in imaging perforators, pedicles and recipient vessels across a wide range of flap types and donor sites. CTA has a range of clinical applications in autologous breast reconstruction, and can aid operative planning and improve outcomes.

The importance of the superficial venous anatomy of the abdominal wall in planning a superficial inferior epigastric artery (SIEA) flap: case report and clinical study

The importance of the venous drainage of the anterior abdominal wall to free tissue transfer in deep inferior epigastric artery perforator flap surgery has been highlighted in several recent publications in this journal, however the same attention has not been given to superficial inferior epigastric artery (SIEA) flaps, in which the flap necessarily relies on the superficial venous drainage. We describe a unique case, in which the presence of two superficial inferior epigastric veins (SIEVs) draining into separate venous trunks was identified. The use of only one trunk led to a well-demarcated zone of venous congestion. A clinical study was also conducted, assessing 200 hemiabdominal walls with preoperative computed tomographic angiography imaging. The presence of more than a single major SIEV trunk was present in 80 hemiabdominal walls (40% of overall sides). There was considerable variability in the source of drainage of the SIEV, draining variably into the deep inferior epigastric vein, the great saphenous vein, the saphenous bulb, a common trunk with the superficial circumflex iliac vein or a common trunk with a second branch of the SIEV. These findings highlight the considerable variation in the number of SIEV trunks as well as their source of regional drainage, and show the importance of consideration of such variation.

The variability of the Superficial Inferior Epigastric Artery (SIEA) and its angiosome: A clinical anatomical study

INTRODUCTION

The superficial inferior epigastric artery (SIEA) is a useful pedicle in supply to the lower abdominal integument, with its use sparing damage to rectus abdominis muscle or sheath. However, it is limited in usefulness due to its anatomical variability. While previous anatomical studies have been limited in number and study design, the use of preoperative imaging has enabled the analysis of this vasculature in large numbers and greater anatomical detail.

METHODS

A clinical anatomical study of 500 hemi-abdominal walls in 250 consecutive patients undergoing preoperative computed tomographic angiography (CTA) prior to autologous breast reconstruction was undertaken. The presence, size, location, and branching pattern of the SIEA were assessed in each case.

RESULTS

The SIEA was identified in 468 cases, an incidence of 94%. Its mean diameter was 0.6 mm, and in 24% of cases was of a diameter >1.5 mm. SIEA location was highly variable, with mean position 2-cm lateral to the linea semilunaris (range 0-8 cm lateral), and relationship to the superficial inferior epigastric vein (SIEV) was also highly variable, with the distance between them ranging from 0.3 to 8.5 cm apart. SIEA branches directly crossed the abdominal midline in 5% of cases. Larger SIEA diameters correlated with a decrease in diameter of ipsilateral DIEA perforators.

CONCLUSION

The SIEA is present more frequently than previously demonstrated, but is typically too small for use in free tissue transfer. The variable degree of SIEA branching suggests that its territory of supply is also variable, and that preoperative imaging may be useful in planning SIEA flaps.

Sequencing delivers diminishing returns for homology detection: implications for mapping the protein universe

MOTIVATION

Databases of sequenced genomes are widely used to characterize the structure, function and evolutionary relationships of proteins. The ability to discern such relationships is widely expected to grow as sequencing projects provide novel information, bridging gaps in our map of the protein universe.

RESULTS

We have plotted our progress in protein sequencing over the last two decades and found that the rate of novel sequence discovery is in a sustained period of decline. Consequently, PSI-BLAST, the most widely used method to detect remote evolutionary relationships, which relies upon the accumulation of novel sequence data, is now showing a plateau in performance. We interpret this trend as signalling our approach to a representative map of the protein universe and discuss its implications.

The efficacy of postoperative monitoring: a single surgeon comparison of clinical monitoring and the implantable Doppler probe in 547 consecutive free flaps

BACKGROUND

An important element in achieving high success rates with free flap surgery has been the use of different techniques for monitoring flaps postoperatively as a means to detecting vascular compromise. Successful monitoring of the vascular pedicle to a flap can potentiate rapid return to theater in the setting of compromise, with the potential to salvage the flap. There is little evidence that any technique offers any advantage over clinical monitoring alone.

METHODS

A consecutive series of 547 patients from a single plastic surgical unit who underwent a fasciocutaneous free flap operation for breast reconstruction [deep inferior epigastric artery perforator (DIEP) flap, superficial inferior epigastric artery (SIEA) flap, or superior gluteal artery perforator (SGAP) flap] were included. A comparison was made between the first 426 consecutive patients in whom flap monitoring was performed using clinical monitoring alone and the subsequent 121 patients in whom monitoring was achieved with the Cook-Swartz implantable Doppler probe. Outcome measures included flap salvage rate and false-positive rate.

RESULTS

There was a strong trend toward improved salvage rates with the implantable Doppler probe compared with clinical monitoring (80% vs. 66%, P = 0.48). When combined with the literature (meta-analysis), the data prove statistically significant (P < 0.01). There was no statistical difference between the groups for false-positive rates.

CONCLUSION

Flap monitoring with the implantable Doppler probe can improve flap salvage rates without increasing the rate of false-positive takebacks.

Postoperative monitoring of free flaps in autologous breast reconstruction: a multicenter comparison of 398 flaps using clinical monitoring, microdialysis, and the implantable Doppler probe

Many techniques for flap monitoring following free tissue transfer have been described; however, there is little evidence that any of these techniques allow for greater rates of flap salvage over clinical monitoring alone. We sought to compare three established monitoring techniques across three experienced microsurgical centers in a comparable cohort of patients. A retrospective, matched cohort study of 398 consecutive free flaps in 347 patients undergoing autologous breast reconstruction was undertaken across three institutions during the same 3-year period, with a single form of postoperative monitoring used at each institution: clinical monitoring alone, the Cook-Swartz implantable Doppler probe, or microdialysis. Both objective and subjective measures of efficacy were assessed. Clinical monitoring alone, the implantable Doppler probe, and microdialysis showed statistically similar rates of flap salvage. False-negative rates were also statistically similar (only seen in the clinically monitored group). However, there was a statistically significant increase in false-positive alarms causing needless take-backs to theater in the microdialysis and implantable Doppler arms, P < 0.001. This study did not find any technique superior to clinical monitoring alone. New monitoring technologies should be compared objectively with clinical monitoring as the current standard in postoperative flap monitoring.

Evaluating anatomical research in surgery: a prospective comparison of cadaveric and living anatomical studies of the abdominal wall

BACKGROUND

Cadaveric research has widely influenced our understanding of clinical anatomy. However, while many soft-tissue structures remain quiescent after death, other tissues, such as viscera, undergo structural and functional changes that may influence their use in predicting living anatomy. In particular, our understanding of vascular anatomy has been based upon cadaveric studies, in which vascular tone and flow do not match the living situation.

METHODS

An angiographic analysis of the abdominal wall vasculature was performed using plain film and computed tomography angiography in 60 cadaveric hemi-abdominal walls (from 31 cadavers) and 140 living hemi-abdominal walls (in 70 patients). The deep inferior epigastric artery (DIEA) and all of its perforating branches larger than 0.5 mm were analysed for number, calibre and location.

RESULTS

Both large, named vessels and small calibre vessels show marked differences between living anatomy and cadaveric specimens. The DIEA was of larger diameter (4.2 mm versus 3.1 mm, P < 0.01) and had more detectable branches in the cadaveric specimens. Perforators were of greater calibre (diameter 1.5 mm versus 0.8 mm, P < 0.01) and were more plentiful (16 versus 6, P < 0.01) in cadaveric specimens. However, the location of individual vessels was similar.

CONCLUSIONS

Cadaveric anatomy displays marked differences to in vivo anatomy, with the absence of living vascular dynamics affecting vessel diameters in cadaveric specimens. Blood vessels are of greater measurable calibre in cadaveric specimens than in the living. Consequently, cadaveric anatomy should be interpreted with consideration of post-mortem changes, while living anatomical studies, particularly with the use of imaging technologies, should be embraced in anatomical research.

A novel tool for intralymphatic injection: the modified glass hypodermic needle

The use of contrast lymphangiography is a relatively new technique in lymphatic anatomical research, employed as a tool for evaluating lymphatic anatomy in fresh cadaveric specimens. With the use of microsurgical techniques to cannulate lymphatics, contrast media can enable the use of lymphangiography for evaluating lymphatic anatomy. However, the ability to cannulate lymphatics with diameters that are less than the smallest commercially available needles has been a significant limitation, and indeed a challenge. The smallest commercially available hypodermic needles have been 30-gauge needles, with 0.3 mm outer diameters. The lymphatics for cannulation in our studies are of the order of 0.1 mm, and other options have been required. We describe a novel technique for cannulating lymphatic vessels, creating a modified glass hypodermic needle. We have shown that these glass needles can be made with accuracy to diameters as low as 0.01 mm. Although 0.1 mm glass needles are the more commonly utilized in most dissections, we can now accurately create these glass needles to any caliber between 0.01 mm and 0.1 mm, based on the predicted lymphatic anatomy.

Macrovascular arteriovenous shunts (MAS): a newly identified structure in the abdominal wall with implications for thermoregulation and free tissue transfer

Microscopic arteriovenous anastomoses are known structures that have many clinical implications, with disease states such as Reynaud's phenomenon and erythromelalgia known consequences of their abnormal functioning. These pre-capillary arteriovenous communications result in increased regional blood flow at the time of capillary filling. Recent advances in imaging technology, providing physiological and anatomical data, have identified a previously undescribed anatomical structure, that of large-vessel (macroscopic) arteriovenous communications, with profoundly different implications. Computed tomographic angiography (CTA) of the abdominal wall vasculature was undertaken in 140 patients prior to reconstructive surgery. All scans were arterial phase, demonstrating functional arteriovenous communications in all patients. These communications identified vascular shunting occurring prior to capillary filling. Fine-cut slices were able to visualise the structures, demonstrate their size as macroscopic (>1 mm diameter) and map the course of the arteriovenous communications. The potential clinical implications and therapeutic possibilities in a range of medical and surgical conditions are described.