Quantifying effectiveness and best practices for bumblebee identification from photographs

Understanding pollinator networks requires species level data on pollinators. New photographic approaches to identification provide avenues to data collection that reduce impacts on declining bumblebee species, but limited research has addressed their accuracy. Using blind identification of 1418 photographed bees, of which 561 had paired specimens, we assessed identification and agreement across 20 bumblebee species netted in Montana, North Dakota, and South Dakota by people with minimal training. An expert identified 92.4% of bees from photographs, whereas 98.2% of bees were identified from specimens. Photograph identifiability decreased for bees that were wet or matted; bees without clear pictures of the abdomen, side of thorax, or top of thorax; bees photographed with a tablet, and for species with more color morphs. Across paired specimens, the identification matched for 95.1% of bees. When combined with a second opinion of specimens without matching identifications, data suggested a similar misidentification rate (2.7% for photographs and 2.5% specimens). We suggest approaches to maximize accuracy, including development of rulesets for collection of a subset of specimens based on difficulty of identification and to address cryptic variation, and focused training on identification that highlights detection of species of concern and species frequently confused in a study area.

Neoadjuvant weekly paclitaxel and carboplatin with trastuzumab and pertuzumab in HER2-positive breast cancer: a Brown University Oncology Research Group (BrUOG) study

PURPOSE

In HER2-positive breast cancer (HER2+ BC), neoadjuvant chemotherapy (NACT) with dual HER2-targeted therapy achieves high pathologic complete response (pCR) rates. Anthracycline-free NACT regimens avoid toxicities associated with anthracyclines, but every 3-week TCHP also has substantial side effects. We hypothesized that a weekly regimen might have equivalent efficacy with less toxicity; we also investigated whether poorly responding patients would benefit from switching to AC.

METHODS

Patients with clinical stage II-III HER2+ BC received weekly paclitaxel 80 mg/m² and carboplatin AUC2 with every 3-week trastuzumab and pertuzumab (wPCbTP), with the option of splitting the pertuzumab loading dose. After 12 weeks, responding patients continued wPCbTP for another 6 weeks, while non-responders switched to AC. Dose modifications and post-op therapy were at investigator discretion.

RESULTS

In 30 evaluable patients, the pCR rate was 77% (95% CI 58-90%); 12/14 (86%) in ER-negative and 11/16 (69%) in ER-positive. Only two patients transitioned to AC for non-response, of which one achieved pCR. There were no episodes of febrile neutropenia or grade ≥ 3 peripheral neuropathy, though several patients who continued wPCbTP stopped before week 18. Split-dose pertuzumab was associated with less grade ≥ 2 diarrhea (40%) than the standard loading dose (60%).

CONCLUSION

pCR rates with our regimen were as high as reported with TCHP with fewer grade ≥ 3 toxicities, though diarrhea remains a concern. Too few patients had a suboptimal response to adequately test switching to AC. The wPCbTP regimen should be considered an alternative to TCHP as neoadjuvant therapy for HER2+ BC.

TRAIL REGISTRATION

ClinicalTrials.gov identifier: NCT02789657.

Abstract P2-12-12: Identifying optimal candidates for three-dimensional bioabsorbable marker placement during breast cancer treatment: Incidence and predictors of postoperative complications

OBJECTIVES: Radiation therapy (RT) is often an integral component of postoperative breast cancer management. Three dimensional (3D) bioabsorbable markers have been designed to assist CT-based tumor bed targeting during the RT process. There have been limited reports detailing complications following placement of such devices. This retrospective analysis attempts to identify demographic and treatment characteristics associated with complications after 3D bioabsorbable marker placement in a cohort of breast cancer patients treated at an academic medical center. METHODS: Records of 160 patients receiving a 3D bioabsorbable marker during initial breast surgery for DCIS or breast cancer were reviewed. Ten devices were removed at subsequent re-excision or mastectomy; therefore, 150 patients were ultimately evaluable. Demographic, tumor and operative/treatment characteristics were collected. Variables including body mass index (BMI), diabetes mellitus (DM), smoking, chemotherapy or RT use and excision volume (EV) were analyzed using multivariable logistic regression analysis (MVA). Endpoints included reoperation for wound complications (re-op), receipt of postoperative antibiotics (abx) and clinically palpable 3D bioabsorbable marker. RESULTS: Median follow-up was 8.2 months. Six (6/150, 4%) patients required re-op for wound complications and 5 required 3D bioabsorbable marker removal due to complications. Twenty (20/150, 13.3%) patients received abx for clinically detected postoperative wound infections. At last follow-up, 61 (61/150, 40.6%) patients noted persistent perceived fullness of the device at the lumpectomy site, and the 3D bioabsorbable marker remained palpable by the physician in 95 (95/150, 63.3%) patients. On MVA, DM and larger EV were associated with greater rates of re-op (p=0.020 and 0.012, respectively, Table 1). Mean EV was 279 cc among the re-op cohort and 85.5 cc among the no re-op cohort. DM, receipt of chemotherapy and larger EV were associated with postoperative abx prescription (p=0.005, 0.009 and 0.005, respectively, Table 2). Mean EV was 169.6 cc among those who received abx and 81.5 cc among those who did not. Larger EV was the only statistically significant predictor of a clinically palpable bioabsorbable marker during follow-up (p=0.044).

Table 1. Multivariable Analysis: Reoperation for Wound ComplicationsVariablep-valueBMI0.986Diabetes0.020Smoking0.999Excision Volume0.012Chemotherapy0.079Radiation0.113

Interchromosomal core duplicons drive both evolutionary instability and disease susceptibility of the Chromosome 8p23.1 region

Recurrent rearrangements of Chromosome 8p23.1 are associated with congenital heart defects and developmental delay. The complexity of this region has led to inconsistencies in the current reference assembly, confounding studies of genetic variation. Using comparative sequence-based approaches, we generated a high-quality 6.3-Mbp alternate reference assembly of an inverted Chromosome 8p23.1 haplotype. Comparison with nonhuman primates reveals a 746-kbp duplicative transposition and two separate inversion events that arose in the last million years of human evolution. The breakpoints associated with these rearrangements map to an ape-specific interchromosomal core duplicon that clusters at sites of evolutionary inversion (P = 7.8 × 10⁻⁵). Refinement of microdeletion breakpoints identifies a subgroup of patients that map to the same interchromosomal core involved in the evolutionary formation of the duplication blocks. Our results define a higher-order genomic instability element that has shaped the structure of specific chromosomes during primate evolution contributing to rearrangements associated with inversion and disease.

Sequencing of the human IG light chain loci from a hydatidiform mole BAC library reveals locus-specific signatures of genetic diversity

Germline variation at immunoglobulin (IG) loci is critical for pathogen-mediated immunity, but establishing complete haplotype sequences in these regions has been problematic because of complex sequence architecture and diploid source DNA. We sequenced BAC clones from the effectively haploid human hydatidiform mole cell line, CHM1htert, across the light chain IG loci, kappa (IGK) and lambda (IGL), creating single haplotype representations of these regions. The IGL haplotype generated here is 1.25 Mb of contiguous sequence, including four novel IGLV alleles, one novel IGLC allele, and an 11.9-kb insertion. The CH17 IGK haplotype consists of two 644 kb proximal and 466 kb distal contigs separated by a large gap of unknown size; these assemblies added 49 kb of unique sequence extending into this gap. Our analysis also resulted in the characterization of seven novel IGKV alleles and a 16.7-kb region exhibiting signatures of interlocus sequence exchange between distal and proximal IGKV gene clusters. Genetic diversity in IGK/IGL was compared with that of the IG heavy chain (IGH) locus within the same haploid genome, revealing threefold (IGK) and sixfold (IGL) higher diversity in the IGH locus, potentially associated with increased levels of segmental duplication and the telomeric location of IGH.

Complete haplotype sequence of the human immunoglobulin heavy-chain variable, diversity, and joining genes and characterization of allelic and copy-number variation

The immunoglobulin heavy-chain locus (IGH) encodes variable (IGHV), diversity (IGHD), joining (IGHJ), and constant (IGHC) genes and is responsible for antibody heavy-chain biosynthesis, which is vital to the adaptive immune response. Programmed V-(D)-J somatic rearrangement and the complex duplicated nature of the locus have impeded attempts to reconcile its genomic organization based on traditional B-lymphocyte derived genetic material. As a result, sequence descriptions of germline variation within IGHV are lacking, haplotype inference using traditional linkage disequilibrium methods has been difficult, and the human genome reference assembly is missing several expressed IGHV genes. By using a hydatidiform mole BAC clone resource, we present the most complete haplotype of IGHV, IGHD, and IGHJ gene regions derived from a single chromosome, representing an alternate assembly of ∼1 Mbp of high-quality finished sequence. From this we add 101 kbp of previously uncharacterized sequence, including functional IGHV genes, and characterize four large germline copy-number variants (CNVs). In addition to this germline reference, we identify and characterize eight CNV-containing haplotypes from a panel of nine diploid genomes of diverse ethnic origin, discovering previously unmapped IGHV genes and an additional 121 kbp of insertion sequence. We genotype four of these CNVs by using PCR in 425 individuals from nine human populations. We find that all four are highly polymorphic and show considerable evidence of stratification (Fst = 0.3-0.5), with the greatest differences observed between African and Asian populations. These CNVs exhibit weak linkage disequilibrium with SNPs from two commercial arrays in most of the populations tested.

The western painted turtle genome, a model for the evolution of extreme physiological adaptations in a slowly evolving lineage

BACKGROUND

We describe the genome of the western painted turtle, Chrysemys picta bellii, one of the most widespread, abundant, and well-studied turtles. We place the genome into a comparative evolutionary context, and focus on genomic features associated with tooth loss, immune function, longevity, sex differentiation and determination, and the species' physiological capacities to withstand extreme anoxia and tissue freezing.

RESULTS

Our phylogenetic analyses confirm that turtles are the sister group to living archosaurs, and demonstrate an extraordinarily slow rate of sequence evolution in the painted turtle. The ability of the painted turtle to withstand complete anoxia and partial freezing appears to be associated with common vertebrate gene networks, and we identify candidate genes for future functional analyses. Tooth loss shares a common pattern of pseudogenization and degradation of tooth-specific genes with birds, although the rate of accumulation of mutations is much slower in the painted turtle. Genes associated with sex differentiation generally reflect phylogeny rather than convergence in sex determination functionality. Among gene families that demonstrate exceptional expansions or show signatures of strong natural selection, immune function and musculoskeletal patterning genes are consistently over-represented.

CONCLUSIONS

Our comparative genomic analyses indicate that common vertebrate regulatory networks, some of which have analogs in human diseases, are often involved in the western painted turtle's extraordinary physiological capacities. As these regulatory pathways are analyzed at the functional level, the painted turtle may offer important insights into the management of a number of human health disorders.

Evolution of human-specific neural SRGAP2 genes by incomplete segmental duplication

Gene duplication is an important source of phenotypic change and adaptive evolution. We leverage a haploid hydatidiform mole to identify highly identical sequences missing from the reference genome, confirming that the cortical development gene Slit-Robo Rho GTPase-activating protein 2 (SRGAP2) duplicated three times exclusively in humans. We show that the promoter and first nine exons of SRGAP2 duplicated from 1q32.1 (SRGAP2A) to 1q21.1 (SRGAP2B) ∼3.4 million years ago (mya). Two larger duplications later copied SRGAP2B to chromosome 1p12 (SRGAP2C) and to proximal 1q21.1 (SRGAP2D) ∼2.4 and ∼1 mya, respectively. Sequence and expression analyses show that SRGAP2C is the most likely duplicate to encode a functional protein and is among the most fixed human-specific duplicate genes. Our data suggest a mechanism where incomplete duplication created a novel gene function-antagonizing parental SRGAP2 function-immediately "at birth" 2-3 mya, which is a time corresponding to the transition from Australopithecus to Homo and the beginning of neocortex expansion.

Resolving the breakpoints of the 17q21.31 microdeletion syndrome with next-generation sequencing

Recurrent deletions have been associated with numerous diseases and genomic disorders. Few, however, have been resolved at the molecular level because their breakpoints often occur in highly copy-number-polymorphic duplicated sequences. We present an approach that uses a combination of somatic cell hybrids, array comparative genomic hybridization, and the specificity of next-generation sequencing to determine breakpoints that occur within segmental duplications. Applying our technique to the 17q21.31 microdeletion syndrome, we used genome sequencing to determine copy-number-variant breakpoints in three deletion-bearing individuals with molecular resolution. For two cases, we observed breakpoints consistent with nonallelic homologous recombination involving only H2 chromosomal haplotypes, as expected. Molecular resolution revealed that the breakpoints occurred at different locations within a 145 kbp segment of >99% identity and disrupt KANSL1 (previously known as KANSL1). In the remaining case, we found that unequal crossover occurred interchromosomally between the H1 and H2 haplotypes and that this event was mediated by a homologous sequence that was once again missing from the human reference. Interestingly, the breakpoints mapped preferentially to gaps in the current reference genome assembly, which we resolved in this study. Our method provides a strategy for the identification of breakpoints within complex regions of the genome harboring high-identity and copy-number-polymorphic segmental duplication. The approach should become particularly useful as high-quality alternate reference sequences become available and genome sequencing of individuals' DNA becomes more routine.

The evolution of African great ape subtelomeric heterochromatin and the fusion of human chromosome 2

Chimpanzee and gorilla chromosomes differ from human chromosomes by the presence of large blocks of subterminal heterochromatin thought to be composed primarily of arrays of tandem satellite sequence. We explore their sequence composition and organization and show a complex organization composed of specific sets of segmental duplications that have hyperexpanded in concert with the formation of subterminal satellites. These regions are highly copy number polymorphic between and within species, and copy number differences involving hundreds of copies can be accurately estimated by assaying read-depth of next-generation sequencing data sets. Phylogenetic and comparative genomic analyses suggest that the structures have arisen largely independently in the two lineages with the exception of a few seed sequences present in the common ancestor of humans and African apes. We propose a model where an ancestral human-chimpanzee pericentric inversion and the ancestral chromosome 2 fusion both predisposed and protected the chimpanzee and human genomes, respectively, to the formation of subtelomeric heterochromatin. Our findings highlight the complex interplay between duplicated sequences and chromosomal rearrangements that rapidly alter the cytogenetic landscape in a short period of evolutionary time.

Insights into hominid evolution from the gorilla genome sequence

Gorillas are humans’ closest living relatives after chimpanzees, and are of comparable importance for the study of human origins and evolution. Here we present the assembly and analysis of a genome sequence for the western lowland gorilla, and compare the whole genomes of all extant great ape genera. We propose a synthesis of genetic and fossil evidence consistent with placing the human-chimpanzee and human-chimpanzee-gorilla speciation events at approximately 6 and 10 million years ago (Mya). In 30% of the genome, gorilla is closer to human or chimpanzee than the latter are to each other; this is rarer around coding genes, indicating pervasive selection throughout great ape evolution, and has functional consequences in gene expression. A comparison of protein coding genes reveals approximately 500 genes showing accelerated evolution on each of the gorilla, human and chimpanzee lineages, and evidence for parallel acceleration, particularly of genes involved in hearing. We also compare the western and eastern gorilla species, estimating an average sequence divergence time 1.75 million years ago, but with evidence for more recent genetic exchange and a population bottleneck in the eastern species. The use of the genome sequence in these and future analyses will promote a deeper understanding of great ape biology and evolution.

Gorilla genome structural variation reveals evolutionary parallelisms with chimpanzee

Structural variation has played an important role in the evolutionary restructuring of human and great ape genomes. Recent analyses have suggested that the genomes of chimpanzee and human have been particularly enriched for this form of genetic variation. Here, we set out to assess the extent of structural variation in the gorilla lineage by generating 10-fold genomic sequence coverage from a western lowland gorilla and integrating these data into a physical and cytogenetic framework of structural variation. We discovered and validated over 7665 structural changes within the gorilla lineage, including sequence resolution of inversions, deletions, duplications, and mobile element insertions. A comparison with human and other ape genomes shows that the gorilla genome has been subjected to the highest rate of segmental duplication. We show that both the gorilla and chimpanzee genomes have experienced independent yet convergent patterns of structural mutation that have not occurred in humans, including the formation of subtelomeric heterochromatic caps, the hyperexpansion of segmental duplications, and bursts of retroviral integrations. Our analysis suggests that the chimpanzee and gorilla genomes are structurally more derived than either orangutan or human genomes.

Detailed analysis of a contiguous 22-Mb region of the maize genome

Most of our understanding of plant genome structure and evolution has come from the careful annotation of small (e.g., 100 kb) sequenced genomic regions or from automated annotation of complete genome sequences. Here, we sequenced and carefully annotated a contiguous 22 Mb region of maize chromosome 4 using an improved pseudomolecule for annotation. The sequence segment was comprehensively ordered, oriented, and confirmed using the maize optical map. Nearly 84% of the sequence is composed of transposable elements (TEs) that are mostly nested within each other, of which most families are low-copy. We identified 544 gene models using multiple levels of evidence, as well as five miRNA genes. Gene fragments, many captured by TEs, are prevalent within this region. Elimination of gene redundancy from a tetraploid maize ancestor that originated a few million years ago is responsible in this region for most disruptions of synteny with sorghum and rice. Consistent with other sub-genomic analyses in maize, small RNA mapping showed that many small RNAs match TEs and that most TEs match small RNAs. These results, performed on approximately 1% of the maize genome, demonstrate the feasibility of refining the B73 RefGen_v1 genome assembly by incorporating optical map, high-resolution genetic map, and comparative genomic data sets. Such improvements, along with those of gene and repeat annotation, will serve to promote future functional genomic and phylogenomic research in maize and other grasses.

Evolutionary toggling of the MAPT 17q21.31 inversion region

Using comparative sequencing approaches, we investigated the evolutionary history of the European-enriched 17q21.31 MAPT inversion polymorphism. We present a detailed, BAC-based sequence assembly of the inverted human H2 haplotype and compare it to the sequence structure and genetic variation of the corresponding 1.5-Mb region for the noninverted H1 human haplotype and that of chimpanzee and orangutan. We found that inversion of the MAPT region is similarly polymorphic in other great ape species, and we present evidence that the inversions occurred independently in chimpanzees and humans. In humans, the inversion breakpoints correspond to core duplications with the LRRC37 gene family. Our analysis favors the H2 configuration and sequence haplotype as the likely great ape and human ancestral state, with inversion recurrences during primate evolution. We show that the H2 architecture has evolved more extensive sequence homology, perhaps explaining its tendency to undergo microdeletion associated with mental retardation in European populations.

Punctuated duplication seeding events during the evolution of human chromosome 2p11

Primate genomic sequence comparisons are becoming increasingly useful for elucidating the evolutionary history and organization of our own genome. Such studies are particularly informative within human pericentromeric regions--areas of particularly rapid change in genomic structure. Here, we present a systematic analysis of the evolutionary history of one approximately 700-kb region of 2p11, including the first autosomal transition from pericentromeric sequence to higher-order alpha-satellite DNA. We show that this region is composed of segmental duplications corresponding to 14 ancestral segments ranging in size from 4 kb to approximately 115 kb. These duplicons show 94%-98.5% sequence identity to their ancestral loci. Comparative FISH and phylogenetic analysis indicate that these duplicons are differentially distributed in human, chimpanzee, and gorilla genomes, whereas baboon has a single putative ancestral locus for all but one of the duplications. Our analysis supports a model where duplicative transposition events occurred during a narrow window of evolution after the separation of the human/ape lineage from the Old World monkeys (10-20 million years ago). Although dramatic secondary dispersal events occurred during the radiation of the human, chimpanzee, and gorilla lineages, duplicative transposition seeding events of new material to this particular pericentromeric region abruptly ceased after this time period. The multiplicity of initial duplicative transpositions prior to the separation of humans and great-apes suggests a punctuated model for the formation of highly duplicated pericentromeric regions within the human genome. The data further indicate that factors other than sequence are important determinants for such bursts of duplicative transposition from the euchromatin to pericentromeric regions.

Generation and annotation of the DNA sequences of human chromosomes 2 and 4

Human chromosome 2 is unique to the human lineage in being the product of a head-to-head fusion of two intermediate-sized ancestral chromosomes. Chromosome 4 has received attention primarily related to the search for the Huntington's disease gene, but also for genes associated with Wolf-Hirschhorn syndrome, polycystic kidney disease and a form of muscular dystrophy. Here we present approximately 237 million base pairs of sequence for chromosome 2, and 186 million base pairs for chromosome 4, representing more than 99.6% of their euchromatic sequences. Our initial analyses have identified 1,346 protein-coding genes and 1,239 pseudogenes on chromosome 2, and 796 protein-coding genes and 778 pseudogenes on chromosome 4. Extensive analyses confirm the underlying construction of the sequence, and expand our understanding of the structure and evolution of mammalian chromosomes, including gene deserts, segmental duplications and highly variant regions.

A physical map of the chicken genome

Strategies for assembling large, complex genomes have evolved to include a combination of whole-genome shotgun sequencing and hierarchal map-assisted sequencing. Whole-genome maps of all types can aid genome assemblies, generally starting with low-resolution cytogenetic maps and ending with the highest resolution of sequence. Fingerprint clone maps are based upon complete restriction enzyme digests of clones representative of the target genome, and ultimately comprise a near-contiguous path of clones across the genome. Such clone-based maps are used to validate sequence assembly order, supply long-range linking information for assembled sequences, anchor sequences to the genetic map and provide templates for closing gaps. Fingerprint maps are also a critical resource for subsequent functional genomic studies, because they provide a redundant and ordered sampling of the genome with clones. In an accompanying paper we describe the draft genome sequence of the chicken, Gallus gallus, the first species sequenced that is both a model organism and a global food source. Here we present a clone-based physical map of the chicken genome at 20-fold coverage, containing 260 contigs of overlapping clones. This map represents approximately 91% of the chicken genome and enables identification of chicken clones aligned to positions in other sequenced genomes.

Analysis of human mRNAs with the reference genome sequence reveals potential errors, polymorphisms, and RNA editing

The NCBI Reference Sequence (RefSeq) project and the NIH Mammalian Gene Collection (MGC) together define a set of approximately 30,000 nonredundant human mRNA sequences with identified coding regions representing 17,000 distinct loci. These high-quality mRNA sequences allow for the identification of transcribed regions in the human genome sequence, and many researchers accept them as the correct representation of each defined gene sequence. Computational comparison of these mRNA sequences and the recently published essentially finished human genome sequence reveals several thousand undocumented nonsynonymous substitution and frame shift discrepancies between the two resources. Additional analysis is undertaken to verify that the euchromatic human genome is sufficiently complete--containing nearly the whole mRNA collection, thus allowing for a comprehensive analysis to be undertaken. Many of the discrepancies will prove to be genuine polymorphisms in the human population, somatic cell genomic variants, or examples of RNA editing. It is observed that the genome sequence variant has significant additional support from other mRNAs and ESTs, almost four times more often than does the mRNA variant, suggesting that the genome sequence is more accurate. In approximately 15% of these cases, there is substantial support for both variants, suggestive of an undocumented polymorphism. An initial screening against a 24-individual genomic DNA diversity panel verified 60% of a small set of potential single nucleotide polymorphisms from which successful results could be obtained. We also find statistical evidence that a few of these discrepancies are due to RNA editing. Overall, these results suggest that the mRNA collections may contain a substantial number of errors. For current and future mRNA collections, it may be prudent to fully reconcile each genome sequence discrepancy, classifying each as a polymorphism, site of RNA editing or somatic cell variation, or genome sequence error.

The DNA sequence of human chromosome 7

Human chromosome 7 has historically received prominent attention in the human genetics community, primarily related to the search for the cystic fibrosis gene and the frequent cytogenetic changes associated with various forms of cancer. Here we present more than 153 million base pairs representing 99.4% of the euchromatic sequence of chromosome 7, the first metacentric chromosome completed so far. The sequence has excellent concordance with previously established physical and genetic maps, and it exhibits an unusual amount of segmentally duplicated sequence (8.2%), with marked differences between the two arms. Our initial analyses have identified 1,150 protein-coding genes, 605 of which have been confirmed by complementary DNA sequences, and an additional 941 pseudogenes. Of genes confirmed by transcript sequences, some are polymorphic for mutations that disrupt the reading frame.

Initial sequencing and comparative analysis of the mouse genome

The sequence of the mouse genome is a key informational tool for understanding the contents of the human genome and a key experimental tool for biomedical research. Here, we report the results of an international collaboration to produce a high-quality draft sequence of the mouse genome. We also present an initial comparative analysis of the mouse and human genomes, describing some of the insights that can be gleaned from the two sequences. We discuss topics including the analysis of the evolutionary forces shaping the size, structure and sequence of the genomes; the conservation of large-scale synteny across most of the genomes; the much lower extent of sequence orthology covering less than half of the genomes; the proportions of the genomes under selection; the number of protein-coding genes; the expansion of gene families related to reproduction and immunity; the evolution of proteins; and the identification of intraspecies polymorphism.

A comparative analysis of lobular and ductal carcinoma of the breast: presentation, treatment, and outcomes

BACKGROUND

Compared with invasive ductal carcinoma, invasive lobular carcinoma of the breast is considered by many to be a more indistinct and multicentric form of cancer that is detected later and is treated less optimally by breast-preservation techniques. This study analyzed the presentation, treatment trends, and survival rates of women who had invasive lobular and ductal breast carcinoma. The objective was to determine the utility of breast-preservation therapy for invasive lobular carcinoma by analysis of historic data on tumor features and survival.

STUDY DESIGN

Data on 291,273 women diagnosed with invasive carcinoma between 1985 and 1993 were obtained from the National Cancer Data Base. Analysis included the patient's age at diagnosis; tumor histology, anatomic site, diameter, grade, and stage; treatment; and disease status 5 years after diagnosis.

RESULTS

The mean patient age at diagnosis was 61.0 years for invasive ductal carcinoma, 63.0 years for invasive lobular carcinoma, and 60.6 years for tumors with combined histology. The anatomic location, tumor diameter, and tumor grade were similar for each histotype. Breast-preservation therapy was less frequent for invasive lobular carcinoma. The 5-year overall survival and local disease-free survival rates for women treated with breast preservation were similar for invasive ductal carcinoma (84% overall survival; 97% disease-free survival) and invasive lobular carcinoma (87% overall survival; 98% disease-free survival).

CONCLUSIONS

Invasive lobular carcinoma presents with a similar age distribution, anatomic subsite, diameter, and grade as invasive ductal carcinoma. Breast preservation is selected less commonly for women who have invasive lobular carcinoma, but this choice of therapy does not compromise the disease-free or overall survival status of this group of patients.

Surgery for early and minimally invasive breast cancer

An increasing number of early and minimally invasive breast cancers are being detected by mammography screening. The role of image-guided core biopsy in nonpalpable breast lesion evaluation is being defined, with issues of cost-effectiveness, diagnostic accuracy, and ability to direct definitive management remaining to be elucidated. The long-term efficacy of breast conservation therapy for early breast cancer continues to be confirmed. Review of special issues in breast conservation therapy demonstrates no benefit to eliminating adjunctive radiation therapy or to limiting therapy in the elderly patient with breast cancer. The distribution of cancer in the duct-lobular system indicates the potential for radical segmental extension. It also influences local recurrence following breast-conserving surgery. Sentinel lymph node dissection may supplant standard axillary dissection as a major prognostic determinant of metastatic disease. These areas of scientific investigation continue to define the role of surgery in early and minimally invasive breast cancer.

Comorbidity risk parameters associated with advanced breast cancer and systemic disease. Management of nonbreast disease

The comorbidity risks associated with advanced breast cancer and systemic disease have been outlined under three broad categories: the local or regional consequences of advanced local breast cancer and its management, systemic sequelae of adjuvant chemotherapy and radiotherapy, and systemic sequelae of metastatic breast disease. Awareness of the potential risks, early detection, and active intervention may diminish the adverse consequences of comorbidities in breast cancer and improve the patient's quality of life.

The renal effects of low-dose dopamine in thermally injured patients

The renal effects of low-dose dopamine (LDD) therapy in hyperdynamic thermally injured patients are unknown. We investigated the renal effects of LDD in ten burn patients (mean +/- SEM age and % total body surface burned: 30.2 +/- 3.3 years and 53.4% +/- 7%) and six controls (mean age; 20.2 +/- 0.5 years). Administration of LDD significantly increased glomerular filtration rate, effective renal plasma flow, sodium excretion, and urine flow in the controls and effective renal plasma flow, urine flow, heart rate, and cardiac index in the patients. The chronotropic effect of dopamine appears to be a principal contributor to the patients' increased effective renal plasma flow. Sodium excretion was increased by LDD only in the patients in whom the predopamine sodium excretion exceeded 5 mEq/h. Lack of a consistent natriuretic effect and the consistent chronotropic effect suggest that the routine use of low-dose dopamine in burn patients is unwarranted. The side effects that attend the desired response determine clinical use, i.e., the potential for blood flow redistribution and increased cardiac work demands must be balanced against increased renal plasma flow and natriuresis.

Prophylactic use of high-frequency percussive ventilation in patients with inhalation injury

Death and the incidence of pneumonia are significantly increased in burn patients with inhalation injury, despite application of conventional ventilatory support techniques. The effect of high-frequency percussive ventilation on mortality rate, incidence of pulmonary infection, and barotrauma were studied in 54 burn patients with documented inhalation injury admitted between March 1987 and September 1990 as compared to an historic cohort treated between 1980 and 1984. All patients satisfied clinical criteria for mechanical ventilation. High-frequency percussive ventilation was initiated within 24 hours of intubation. The patients' mean age and burn size were 32.2 years and 47.8%, respectively (ranges, 15 to 88 years; 0% to 90%). The mean number of ventilator days was 15.3 +/- 16.7 (range, 1 to 150 days), with 26% of patients ventilated for more than 2 weeks. Fourteen patients (25.9%) developed pneumonia compared to an historic frequency of 45.8% (p less than 0.005). Mortality rate was 18.5% (10 patients) with an expected historic number of deaths of 23 (95% confidence limits of 17 to 28 deaths). The documented improvement in survival rate and decrease in the incidence of pneumonia in patients treated with prophylactic high-frequency ventilation (HFV), as compared to a cohort of patients treated in the 7 years before the trial, indicates the importance of small airway patency in the pathogenesis of inhalation injury sequelae and supports further use and evaluation of HFV.

Relationship of transfusion and infection in a burn population

The relationship between the number of red blood cell transfusions and major infectious complications was evaluated in 594 thermal injury patients admitted between 1982 and 1986 who had burns over 10% or more of total body surface area and survived more than 10 days. The mean age of this group was 32.9 years, with a mean burn size of 36% of total body surface area; 83% were male. Of the 594 patients, 23.7% died and 38.7% had documented inhalation injury. The mean number of red blood cell transfusions received was 19.7, with a range of 0 to 201. Two hundred fourteen patients (36%) had major infectious complications, defined as pneumonia or invasive burn wound infection. A cross-tabulation of predicted mortality, number of transfusions, and infectious complications revealed a significant positive correlation between transfusion number and infectious complications in patients with predicted mortalities between 10 and 70%. Per cent total burn, patient age, presence of inhalation injury, and number of transfusions were identified by discriminant function analysis as significant variables (p less than 0.05) in discriminating between patients with and without infections (85% accuracy). Logistic regression analysis confirmed the above findings, showing a relationship between the number of transfusions received and infectious morbidity which was independent of age or burn size, but no significant relationship between number of transfusions and mortality.

High-frequency percussive ventilation in patients with inhalation injury

Inhalation injury complicated by bacterial pneumonia is now one of the primary causes of morbidity and mortality in patients with thermal injury. We have investigated the use of high-frequency percussive ventilation (HFPV) as a means of ventilatory support for these patients. We propose that high-frequency ventilation may decrease the incidence of pulmonary infection following inhalation injury and decrease the incidence of iatrogenic barotrauma caused by conventional ventilation. High-frequency ventilation was instituted initially as salvage therapy in a group of five patients. In each case, normocapnia or arterial pO2 saturation of greater than 90% on a FIO2 of 60% or less was achieved with high-frequency ventilation but not with conventional ventilation. A second group of ten patients was prospectively entered into a study on the use of HFPV in patients with inhalation injury. One patient was removed from the study, and one patient was unable to be ventilated because of severely noncompliant lungs. Eight patients with a mean age of 29 years and a mean burn size of 38% of the total body surface completed the protocol. All patients survived, two developed pneumonia, and one developed subcutaneous emphysema. These results suggest that HFPV is effective in the treatment of patients with severe inhalation injury.

Fluid resuscitation of infants and children with massive thermal injury

Age-related limitations of physiologic reserve in burned children make adequacy of intravenous fluid resuscitation critical. To quantify fluid requirements, the medical records of all children admitted to the Army Institute of Surgical Research from 1980 to 1986 whose weight was 25 kilograms or less and burn size was 25% or greater were reviewed to quantify fluid requirements. Forty-three children ranging in age from 1.5-108 months (means 26 +/- 22 m), with 25-89% total body surface burned (TBSB) (means 41.7% +/- 14.6%), met inclusion criteria. The average total volume of fluid received during the first 24 hours was 6.3 +/- 2.2 cc/kg/% TBSB. The net volume of resuscitation fluid, total volume less the calculated maintenance fluid requirements, was 3.91 +/- 2.2 cc/kg/% TBSB. Univariate analysis and linear regression of independent variables including age, weight, per cent full thickness, and inhalation injury revealed each had no significant influence on the volume of resuscitation. We recommend supplying maintenance volume and initiating burn resuscitation at 3 cc/kg/% TBSB.

Regulation of microvillus structure: calcium-dependent solation and cross-linking of actin filaments in the microvilli of intestinal epithelial cells

The bundle of filaments within microvilli of intestinal epithelial cells contains five major proteins including actin, calmodulin, and subunits of 105-, 95-, and 70-kdaltons. It has been previously shown (Howe, C. L., M. S. Mooseker, and T. A. Graves. 1980. Brush-border calmodulin: a major component of the isolated microvillus core. J. Cell Biol. 85: 916-923) that the addition of Ca++ (> 10(-6) M) to microvillus cores causes a rapid, drastic, but at least partially reversible disruption of this actin filament bundle. High-speed centrifugation of microvillus cores treated with Ca++ indicates that several core proteins are solubilized, including 30-50% of the actin and calmodulin, along with much of the 95- and 70-kdalton subunits. Gel filtration of such Ca++ extracts in the presence and absence of Ca++ indicates that microvillar actin "solated" by Ca++ is in an oligomeric state probably complexed with the 95-kdalton subunit. Removal of Ca++ results in the reassembly of F-actin, probably still complexed with 95-kdalton subunit, as determined by gel filtration, cosedimentation, viscometry, and electron microscopy. The 95-kdalton subunit (95K) was purified from Ca++ extracts by DEAE-Sephadex chromatography and its interaction with actin characterized by viscometry, cosedimentation, and EM in the presence and absence of Ca++. In the presence, but not absence, of Ca++, 95K inhibits actin assembly (50% inhibition at 1:50-60 95K to actin) and also reduces the viscosity of F-actin solutions. Similarly, sedimentation of actin is inhibited by 95K, but a small, presumably oligomeric actin- 95K complex formed in the presence of Ca++ is pelletable after long-term centrifugation. In the absence of Ca++, 95K cosediments with F-actin. EM of 95K-actin mixtures reveals that 95K "breaks" actin into small, filamentous fragments in the presence of Ca++. Reassembly of filaments occurs once Ca++ is removed. In the absence of Ca++, 95K has no effect on filament structure and, at relatively high ratios (1:2-6) of 95K to actin, this core protein will aggregate actin filaments into bundles.

Brush-border calmodulin. A major component of the isolated microvillus core

Calmodulin is present in brush borders isolated from intestinal epithelial cells and is one of the major components of the microvillar filament bundle. Calmodulin was purified from either demembranated brush borders or microvilli by a simple boiling procedure. The boiled supernate derived from the microvillus cores contained one major polypeptide of 20,000 daltons. The supernate from the brush-border preparation contained the 20,000-dalton subunit and a second protein of 30,000 daltons. The 20,000-dalton subunit has been identified as calmodulin by several criteria: (a) heat resistance, (b) comigration with brain calmodulin on alkaline urea gels and SDS gels, both cases in which the 20,000-dalton protein, like calmodulin, exhibits a shift in electrophoretic mobility in the presence of Ca++, and (c) 4--5-fold activation of 3',5'-cyclic nucleotide phosphodiesterase in the presence but not the absence of Ca++. With a cosedimentation assay it was determined that brush-border calmodulin does not bind directly to actin. In the presence of Ca++ (greater than 5 x 10(-7) M) there was a partial release of calmodulin from the microvillus core, along with a substantial conversion of microvillus actin into a nonpelletable from. The dissociation of calmodulin was reversed by removal of Ca++. If microvillus cores were pretreated with phalloidin, the Ca++-induced solubilization of actin was prevented, but the partial dissociation of calmodulin still occurred. The molar ratio of calmodulin:actin is 1:10 in the demembranated brush border and 1:2-3 in the microvillus core. No calmodulin was detected in the detergent-solubilized brush-border membrane fraction.