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Biomedical subjects

C Ladd

Publications and source records attributed to C Ladd.

At least 19 recordsLinked to original sources
PubMed2001

Multiclass cancer diagnosis using tumor gene expression signatures.

The optimal treatment of patients with cancer depends on establishing accurate diagnoses by using a complex combination of clinical and histopathological data. In some instances, this task is difficult or impossible because of atypical clinical presentation or histopathology. To determine whether the diagnosis of multiple common adult malignancies could be achieved purely by molecular classification, we subjected 218 tumor samples, spanning 14 common tumor types, and 90 normal tissue samples to oligonucleotide microarray gene expression analysis. The expression levels of 16,063 genes and expressed sequence tags were used to evaluate the accuracy of a multiclass classifier based on a support vector machine algorithm. Overall classification accuracy was 78%, far exceeding the accuracy of random classification (9%). Poorly differentiated cancers resulted in low-confidence predictions and could not be accurately classified according to their tissue of origin, indicating that they are molecularly distinct entities with dramatically different gene expression patterns compared with their well differentiated counterparts. Taken together, these results demonstrate the feasibility of accurate, multiclass molecular cancer classification and suggest a strategy for future clinical implementation of molecular cancer diagnostics.

Biomarkers, Tumor↗
PubMed2001

Classification of human lung carcinomas by mRNA expression profiling reveals distinct adenocarcinoma subclasses.

We have generated a molecular taxonomy of lung carcinoma, the leading cause of cancer death in the United States and worldwide. Using oligonucleotide microarrays, we analyzed mRNA expression levels corresponding to 12,600 transcript sequences in 186 lung tumor samples, including 139 adenocarcinomas resected from the lung. Hierarchical and probabilistic clustering of expression data defined distinct subclasses of lung adenocarcinoma. Among these were tumors with high relative expression of neuroendocrine genes and of type II pneumocyte genes, respectively. Retrospective analysis revealed a less favorable outcome for the adenocarcinomas with neuroendocrine gene expression. The diagnostic potential of expression profiling is emphasized by its ability to discriminate primary lung adenocarcinomas from metastases of extra-pulmonary origin. These results suggest that integration of expression profile data with clinical parameters could aid in diagnosis of lung cancer patients.

Adenocarcinoma↗
PubMed2001

Preservation and collection of biological evidence.

As the courts have placed greater emphasis on physical evidence during the past few decades, the initial stages of evidence examination have become increasingly important to the successful resolution of many criminal investigations. This emphasis on evidence collection and preservation is often manifested by many rigorous court challenges. This article reviews how the ability to introduce DNA test results in court is affected by methods used to recognize, document, collect, and preserve biological evidence.

DNA↗
PubMed2001

Interpretation of complex forensic DNA mixtures.

Forensic evidentiary samples routinely contain DNA from multiple contributors. The interpretation of these mixtures can be a challenging task for the DNA scientist. Several approaches are discussed (no calculation- qualitative statement; probability of exclusion; likelihood ratio estimates; presumptive genotype assignment based on peak heights), which have been employed to assess the significance of an inclusion/match when DNA mixtures have been detected in casework samples. These statistical approaches are discussed in light of technical challenges that can arise when evaluating evidentiary samples.

Criminology↗
PubMed2001

The Green Revolution: botanical contributions to forensics and drug enforcement.

Forensic botany encompasses many sub-disciplines, including plant anatomy, plant ecology, plant systematics, plant molecular biology, palynology, and limnology. Although the field of forensic botany has been recognized since the mid-1900's, the use of trace plant material as physical evidence in criminal casework is still novel. A review of published forensic casework that used plant evidence is presented here. Cases include the analysis of wood evidence in the Charles Lindbergh baby kidnapping, the use of pollen in establishing the location of a sexual assault, and pollen analysis to determine the time of year for burial in a mass grave. Additional cases discuss the use of plant growth rates to determine the time of a body deposit in a field, the use of diatoms to link individuals to a crime scene, and plant DNA typing to match seedpods to a tree under which a body was discovered. New DNA methods in development for plant species identification and individualization for forensic applications are also discussed. These DNA methods may be useful for linking an individual to a crime scene or physical evidence to a geographic location, or tracking marijuana distribution patterns.

Botany↗
PubMed1999

A systematic analysis of PCR contamination.

In light of the strict legal scrutiny surrounding DNA typing at this time, it has become necessary to systematically address the issue of PCR contamination. To precisely define the parameters affecting PCR contamination under casework analysis conditions, PCR amplification reactions were intentionally compromised by employing sub-standard laboratory technique and by introducing secondary sources of DNA. The PCR parameters considered for potential sources of contamination include amplification set-up, amplification product handling, aerosol DNA and storage. In addition, analyst technique was evaluated by modifying or eliminating standard safeguards. Under the circumstances normally encountered during casework analysis, PCR contamination was never noted. Significantly, using the dot blot detection method, contamination was never observed when nanogram quantities of genomic DNA were mishandled or aerosolized. Contamination occurred only when amplification product was carelessly manipulated or purposefully sprayed near or directly into open tubes containing water or genomic DNA. Although standard precautions should be employed during PCR-based DNA typing, our data indicates that contamination during amplification procedures is not prevalent when detected by dot blot analysis.

DNA↗
PubMed1999

NaOH treatment to neutralize inhibitors of Taq polymerase.

The introduction of polymerase chain reaction (PCR) into the forensic field has greatly extended the ability to analyze DNA from small or degraded samples. However, one significant problem with PCR analysis is the sensitivity of Taq Polymerase to inhibitors found in many substrates commonly encountered with evidentiary materials. We hypothesize that the most problematic of these compounds intercalate into double stranded DNA (dsDNA) and have significantly less affinity for single stranded DNA (ssDNA). This study presents a comprehensive analysis of a novel method for the neutralization of Taq inhibitors by denaturation and washing with NaOH in Microcon-100 filtration units. The data show that DNA recovered following NaOH repurification routinely amplifies when other inhibitor neutralization techniques are unsuccessful. Genetic profiles have been obtained with both AmpliType PM + DQA1 and D1S80 systems. However, the NaOH protocol is not advised when the quantity of DNA is limited since the treatment results in significant loss of DNA.

Blood Stains↗
PubMed1999

A systematic analysis of secondary DNA transfer.

The Nature letter by R. van Oorschot and M. Jones (1) addressed two topics: the primary transfer of DNA from person to person or to various objects, and the secondary transfer of DNA through an intermediary. Forensic scientists have described the primary transfer of DNA and other biological evidence for many years. However, the authors also reported detecting secondary transfer of DNA from an object to a person's hands, which could adversely affect DNA typing in the forensic context. The prospect of secondary transfer raises questions of interest to both the legal and forensic communities. Therefore, we sought to evaluate parameters potentially leading to secondary DNA transfer. Our data do not support the conclusion that secondary transfer will compromise DNA typing results under typical forensic conditions.

DNA↗
PubMed1998

Forensic applications of DNA typing: part 2: collection and preservation of DNA evidence.

The initial stages of physical evidence examination are pivotal to the successful resolution of criminal investigations. Recent cases clearly reinforce the notion that methods of evidence collection and preservation will continue to be rigorously scrutinized and challenged in court. This article reviews forensic applications of DNA typing, focusing on the collection and preservation of biological evidence. Topics addressed include physical evidence collection at the crime scene, the forensic laboratory, and the autopsy room. Specific concerns pertaining to different sources of DNA evidence are discussed, as are special collection methods associated with various substrates on which the evidence is deposited.

Body Fluids↗
PubMed1997

DNA extraction from liquid blood using QIAamp.

The implementation of convicted felon DNA databases by increasing numbers of forensic science laboratories has engendered the need for a quick, efficient, and cost-effective method for the isolation of DNA from liquid blood samples. Because of the large numbers of samples involved, the ideal method would combine high throughput capability with maximal yield, high quality, and minimal time. We have found that the QIAGEN QIAamp Blood Kit/Tissue Kit satisfy all of these requirements. This simple, low cost spin column procedure yields purified DNA of approximately 20-30 kb that can be used directly in PCR or other enzymatic reactions without further purification. We compared the QIAamp isolation procedure to the standard SDS-Proteinase K/organic extraction/microcon purification procedure currently used by many forensic laboratories. The QIAamp procedure consistently gave a two- to four-fold increased yield relative to the organic extraction procedure. The DNA obtained was of high molecular weight, exhibited little degradation, and was suitable for RFLP and PCR analyses. We have found QIAGEN's QIAamp DNA isolation procedure to be ideally suited for preparation of samples for DNA databasing.

DNA↗
PubMed1996

A PCR-based strategy for ABO genotype determination.

The ABO blood group system has been widely used in forensic serology. Several techniques have been developed which detect ABH antigens. To overcome the problems associated with conventional methods such as bacterial contamination, extreme environmental conditions, antigen activity, non-secretor issues, and non-specific absorption, several new strategies have been employed to detect ABO genotypes by PCR. We have developed improved amplimers for the glycosyl transferase locus on chromosome 9 and examined the suitability of PCR-based ABO genotyping for forensic identification. We show that the ABO system is primate specific and that DNA extracted from various tissues commonly encountered in criminal cases can be quickly and reliably typed by ABO-PCR. The results indicate that ABO genotyping by PCR and restriction enzyme digestion of the amplified product is a useful procedure for forensic analysis that can provide additional discriminating power compared to conventional immunological methods.

ABO Blood-Group System↗
PubMed1995

Cisplatin, 5-fluorouracil, and ifosfamide in the treatment of recurrent or advanced cervical cancer.

We performed a prospective, phase II trial of cisplatin, 5-fluorouracil, and ifosfamide in the treatment of 30 women with recurrent or advanced cervical cancer. Median age was 47 years old. Twenty-one tumors were squamous and 83% of tumors were grade 2 or 3. Twenty-six patients (87%) received prior pelvic radiotherapy, and six patients (20%) received prior radiation sensitizing chemotherapy. Median time to recurrence was 6 months. In 11 patients (37%) tumor recurred in the pelvis. A combination of cisplatin 90 mg/m2, 5-fluorouracil 1500 mg/m2, and ifosfamide 3 g/m2 was administered intravenously in divided doses over 3 consecutive days every 28 days. Sixteen patients (53%) responded to chemotherapy with a complete response occurring in 5 patients (17%) and a partial response in 11 patients (36%). One of 11 patients (7%) with a pelvic recurrence responded compared to 15 of 19 (79%) with extrapelvic recurrence (P = 0.001). Tumors recurring after 6 months had a higher response rate (73%) compared to those recurring before 6 months (33%) (P = 0.05). Three of the six patients (50%) treated with prior radiation sensitizing chemotherapy responded. Seven of nine patients (78%) with adenocarcinoma responded. Median survival is 12 months (3-36 months). In conclusion, cisplatin, 5-fluorouracil, and ifosfamide resulted in a favorable response rate (53%) and a median survival of 12 months. As expected, patients with extrapelvic recurrence and recurrence after 6 months had an improved response rate while, surprisingly, those receiving prior radiation sensitizing chemotherapy and those with adenocarcinoma did not exhibit a less favorable response rate.

Adenocarcinoma↗
PubMed1994

DNA typing in forensic science. I. Theory and background.

In the last few years, DNA typing procedures have become increasingly important in the fields of forensic science and forensic medicine. This paper reviews background information on DNA and human genetics, and addresses how molecular techniques such as restriction fragment length polymorphism (RFLP) and polymerase chain reaction (PCR) analysis have been used to detect genetic polymorphism in human populations. The systems discussed include single locus RFLP, HLA DQ-alpha, amplified fragment length polymorphism (AMP-FLPs), short tandem repeats (STRs), and mitochondrial DNA typing. Several DNA typing methods have been thoroughly validated for forensic use. With proper control measures, DNA analysis should be considered reliable. At this time, DNA evidence/testimony is generally accepted by the courts and greatly assists in the resolution of criminal and civil investigations.

Body Fluids↗
PubMed1993

Subjective evaluation of function following moderately accelerated rehabilitation of anterior cruciate ligament reconstructed knees.

Rehabilitation protocols following anterior cruciate ligament reconstructions have become increasingly aggressive in the past several years, preparing the patient to return to sport activities within 4 to 6 months. In 1989, we initiated a moderately accelerated protocol and were interested in the long-term effects of early weight bearing, immediate full motion, early incorporation of closed chain activities, and early return to sport. We received responses from 58 of 180 patients surveyed. All had undergone a bone-patellar tendon-bone autograft reconstruction procedure 12 to 21 months prior and had followed the rehabilitation protocol described. Results of the Lysholm Knee Scoring Scale and a questionnaire regarding preinjury and postinjury activity levels, pain and stability ratings, and current activity indicated that the majority of these patients had returned to sport and recreation and were participating at levels of moderate to high intensity with little or no difficulty.

Journal Article↗
PubMed1992

Determination and expression of platelet-derived growth factor-AA in bone cell cultures.

We describe a sensitive technique for the extraction and quantitation of platelet-derived growth factor (PDGF)-AA in serum-free culture medium conditioned by fetal rat osteoblast-enriched (Ob) cells and demonstrate the expression of PDGF-A mRNA in Ob cells. Using C18 Sep-Pak chromatography with a methanol step gradient, we extracted immunoreactive PDGF-AA from the culture medium. A RIA protocol employing a recombinant human PDGF-AA standard enabled us to measure picomolar equivalents of PDGF-AA in Ob cell culture medium. The recovery of recombinant human PDGF-AA was 50 +/- 4%, and the coefficient of variation, including chromatographic extraction, was 15% for intraassay and 8.3% for interassay variability. The polyclonal antibody to recombinant human PDGF-AA displayed approximately 20-30% cross-reactivity with PDGF-AB, but did not bind PDGF-BB or other growth factors and cytokines known to be secreted by bone cells. Medium from Ob cells cultured for 24 h contained 0.9-1.3 pM human PDGF-AA equivalents, and exposure to cycloheximide (3.6 microM) decreased those levels by 65%. Treatment of cells with recombinant human transforming growth factor-beta 1 at 0.04-4 nM for 24 h increased PDGF-AA levels by up to 3.5-fold. Northern blot analysis of RNA from Ob cells revealed the expression of PDGF-A, but not PDGF-B, transcripts, and transforming growth factor-beta 1 at 0.04 and 0.2 nM increased steady state PDGF-A mRNA by 3- to 6-fold. Our studies describe a sensitive and reproducible technique for monitoring PDGF-AA levels in cell-conditioned medium and demonstrate that Ob cells synthesize PDGF-AA.

Animals↗