Genome-wide SNP typing reveals signatures of population history

Single-nucleotide polymorphism (SNP) arrays have become a popular technology for disease-association studies, but they also have potential for studying the genetic differentiation of human populations. Application of the Affymetrix GeneChip Human Mapping 500K Array Set to a population of 102 individuals representing the major ethnic groups in the United States (African, Asian, European, and Hispanic) revealed patterns of gene diversity and genetic distance that reflected population history. We analyzed allelic frequencies at 388,654 autosomal SNP sites that showed some variation in our study population and 10% or fewer missing values. Despite the small size (23-31 individuals) of each subpopulation, there were no fixed differences at any site between any two subpopulations. As expected from the African origin of modern humans, greater gene diversity was seen in Africans than in either Asians or Europeans, and the genetic distance between the Asian and the European populations was significantly lower than that between either of these two populations and Africans. Principal components analysis applied to a correlation matrix among individuals was able to separate completely the major continental groups of humans (Africans, Asians, and Europeans), while Hispanics overlapped all three of these groups. Genes containing two or more markers with extraordinarily high genetic distance between subpopulations were identified as candidate genes for health differences between subpopulations. The results show that, even with modest sample sizes, genome-wide SNP genotyping technologies have great promise for capturing signatures of gene frequency difference between human subpopulations, with applications in areas as diverse as forensics and the study of ethnic health disparities.

RNAi screens reveal novel metabolic regulators: RIP140, MAP4k4 and the lipid droplet associated fat specific protein (FSP) 27

Adipose tissue modulates whole body metabolism and insulin sensitivity by controlling circulating lipid levels and producing molecules that can regulate fatty acid metabolism in such tissues as muscle and liver. We have developed RNA interference (RNAi) screens to identify genes in cultured adipocytes that regulate insulin signalling and key metabolic pathways. These short interfering RNA (siRNA)-based screens identified the transcriptional corepressor receptor interacting protein 140 (RIP140) (J Clin Invest 116: 125, 2006) and the mitogen-activated protein kinase (MAP4k4) (Proc Natl Acad Sci USA 103: 2087, 2006) as negative regulators of insulin-responsive hexose uptake and oxidative metabolism. Gene expression profiling revealed that RIP140 depletion upregulates the expression of clusters of genes in the pathways of glucose uptake, glycolysis, tricarboxylic acid cycle, fatty acid oxidation, mitochondrial biogenesis and oxidative phosphorylation. RIP140-null mice resist weight gain on a high-fat diet and display enhanced glucose tolerance. MAP4k4 depletion in adipocytes increases many of the RIP140-sensitive genes, increases adipogenesis and mediates some actions of tumour necrosis factor-alpha (TNF-alpha). Remarkably, another hit in our RNAi screens was fat specific protein 27 (FSP27), a highly expressed isoform of Cidea. We discovered that FSP27 unexpectedly associates specifically with lipid droplets and regulates fat storage. We conclude that RIP140, MAP4k4 and the novel lipid droplet protein FSP27 are powerful regulators of adipose tissue metabolism and are potential therapeutic targets for controlling metabolic disease. The discovery of these novel proteins validates the power of RNAi screening for discovery of new therapeutic approaches to type 2 diabetes and obesity.

Posterior interosseous artery flap, fasciosubcutaneous pedicle technique: a study of 25 cases

This study was undertaken in an attempt to improve the versatility of the posterior interosseous artery flap (PIA flap) and to decrease flap complication rate. The PIA flap was used for resurfacing 25 cases of the hand and distal forearm over a 2-year period. Observations were made on the anatomy of the PIA flap and its distal reach. Doppler analysis was made a mandatory part of the preoperative planning. Flaps were also raised from the zone of injury if Doppler confirmed the presence of good perforators. No attempt was made to identify the anastomosis between the anterior interosseous artery (AIA) and the PIA prior to flap raising since its presence was ascertained preoperatively with a Doppler and flap raising could begin straightway, saving precious tourniquet time. The surgical technique was further modified to include a large amount of fascia and subcutaneous tissue with the flap. This could perhaps be the reason for survival of larger flaps, absence of venous congestion and the low complication rate seen in our series. These flaps were used to resurface defects involving the dorsum of the hand, palm, distal forearm, wrist and fingers (both dorsal and volar surfaces). The distal reach of the flap was improved by exteriorising the pedicle and bowstringing it across the wrist which was kept in extension. The flap could thus easily reach the distal interphalangeal joint. This exteriorised pedicle was covered with a split thickness skin graft and was divided 3 weeks later under local anaesthesia making it a two-stage procedure. Adipofascial and osteocutaneous PIA flaps were also used depending on the requirement. Out of 25 flaps, 23 were of the adipofascial variety and one each of the fascial and osteocutaneous type. The majority of the patients were between 21 and 30 years old. Trauma was the leading cause of tissue deficit in our series (19/25). Within the trauma group occupational mishap (entrapment of hand in roller machine, presser machine, etc.) was the leading cause, road traffic accident being the next most common. The most common site of defect was the dorsum of the hand (14/25). The largest flap measured 12x8cm and the smallest flap measured 3x2cm. Only three minor complications were noted, two cases of partial flap loss (one of them needing a secondary procedure of debridement and grafting) and one partial graft loss in the case of fascial flap which needed regrafting. Importantly no evidence of venous congestion was noted in any of the flaps.

Critical flicker frequency: diagnostic tool for minimal hepatic encephalopathy

BACKGROUND/AIMS

Minimal hepatic encephalopathy (MHE) is associated with poorer quality of life and increased work disability. Diagnosis requires cumbersome psychometric and neurophysiological tests. We evaluated critical flicker frequency (CFF) to diagnose MHE.

METHODS

156 cirrhotic patients (age 41+/-12.5 yr) without overt encephalopathy (Child A 63, Child B 56, Child C 37) were evaluated by psychometric (number connection tests A, B or figure connection tests A, B), P300 auditory event related potential (ERP) and CFF. MHE was diagnosed by abnormal psychometric and/or P300 auditory event related potential.

RESULTS

Prevalence of MHE was 53% with 27 (43%) in Child's A, 33 (59%) in Child's B and 23 (62%) in Child's C cirrhosis (p=NS). Of 83 patients, 72 (87%) had abnormal psychometry, 64 (77%) had abnormal P300 auditory event related potential (ERP) (380.6+/-28.8 ms) and in 66 (80%) CFF was below 39 Hz. 60 (83%) patients with abnormal psychometry and 51 (80%) with abnormal P300 auditory event related potential had CFF below 39 Hz. CFF sensitivity (96%), specificity (77%) and positive predictive value (68%), negative predictive value (98%) and diagnosis accuracy was 83.3% when compared to patients with both abnormal psychometry and P300ERP.

CONCLUSIONS

Critical flicker frequency is a simple, reliable and accurate test without any age or literacy dependence for the diagnosis of MHE.

N-hexane neuropathy in screen printers

BACKGROUND

To study the clinical and electrophysiological profile of n-hexane neuropathy in a tertiary care center of India.

METHODS

Twenty five screen printers from five different factories, with peripheral neuropathy were included in the study. A detailed general physical, systemic and neurological examination was conducted Visual acuity, color vision and field charting was done in all the subjects. All patients were subjected to Folstein mini mental scale examination. Electrophysiological evaluation included motor and sensory conduction studies of the conventionally studied nerves of upper and lower limbs, Needle EMG of various distal and proximal muscles and patterned visual evoked responses. The electrophysiological profile was repeated every three months till one year. Sural nerve biopsy was studied in six patients. The patients were followed for a maximum of 4 years.

RESULTS

Twenty three [92%] patients had sensory- motor neuropathy, while pure sensory neuropathy was seen in two. The sensory conductions were affected almost equally in upper as well as the lower limbs, while the motor conductions were affected more in the lower limbs than the upper limbs. The sensory conductions were not recordable in both the upper and the lower limbs in 18 [72%] patients. Motor conduction studies revealed an asymmetric and patchy involvement. Proximal conduction block was seen in 3 patients [12%]. On needle EMG features of denervation were seen in all patients. P100 latency was normal in all. Sural nerve biopsy showed a selective decrease in large myelinated axons with demyelination. Axonal swelling with focal areas of demyelination was observed in two patients.

CONCLUSIONS

The electrophysiological patterns as well as the histopathology reflect the pathophysiology of n-hexane neuropathy.

Intramesosigmoid hernia: a rare type of congenital internal hernia

Intestinal obstruction from congenital internal hernias is a rare and often unsuspected problem. We report the case of a 66-year-old male with a rare type of congenital internal hernia causing bowel obstruction. He underwent successful laparoscopy-assisted surgical repair without bowel resection. Symptomatic congenital internal hernias usually present with intermittent or acute small-bowel obstruction without any history of previous abdominal surgery. Laparoscopy or hand-assisted laparoscopy can be useful tools for locating the region of pathology and enable minimally invasive surgical treatment.

Robotically assisted biliary pancreatic diversion with a duodenal switch: a new technique

BACKGROUND

Minimally invasive surgical techniques decrease the length of hospitalization and the morbidity for general surgery procedures. Application of minimally invasive techniques to obesity surgery had previously been limited to stapled techniques used primarily for the Roux-en-Y gastric bypass and laparoscopic band placement. The authors present the technique for totally intracorporeal robotically assisted biliary pancreatic diversion with a duodenal switch (BPD/DS) using five ports.

METHODS

After development of the technique in animal and human cadaver models, the da Vinci robot was first used in October 2000 to perform BPD/DS using five ports and a totally intracorporeal technique. Patient selection was based on standard surgery guidelines for the morbidly obese.

RESULTS

This technique was applied for 47 patients with a mean body mass index (BMI) of 45 kg/m2 and a mean age of 38 +/- 10 years. The median operating time was 514 min (range, 370-931 min). The median operative time for the last 10 patients was 379 min (range, 370-582 min). Three patients underwent conversion to open surgery, and four patients experienced postoperative leaks with no mortality.

CONCLUSION

The safety, feasibility, and reproducibility of a minimally invasive robotic surgical approach to complex abdominal operations such as BPD/DS is demonstrated. The BPD/DS allows for a sutured bowel anastomosis similar to the open technique using a minimal number of small access ports.

Laparoscopic vs conventional tension free inguinal herniorrhaphy: 2005 Society of American Gastrointestinal Endoscopic Surgeons (SAGES) annual meeting debate

This report summarizes the 2005 Society of American Gastrointestinal and Endoscopic Surgeons' inguinal herniorrhaphy debate. Most inguinal herniorrhaphies in the United States are performed using one of several prosthesis-based, tension-free (TFR) procedures. Approximately 15% of the procedures used are laparoscopic inguinal herniorrhaphies (LIH). Technical ease, lower cost, and local anesthesia are the major advantages attributed to TFR, whereas superior cosmesis, less perioperative pain, and a faster return to normal activity is attributed to LIH. The overall cost-benefit ratio, incidence of chronic pain syndromes, and relevance of a recent major trial could not be entirely settled in this debate. The importance of adequate training for surgeons undertaking LIH cannot be overemphasized. Experienced surgeons displaying equivalent results for LIH and TFR are justified in offering LIH to patients with primary unilateral inguinal hernias.

Effects of oestrogen on trigeminal ganglia in culture: implications for hormonal effects on migraine

Although migraine is more common in women than men and often linked to the menstrual cycle, few studies have investigated the biological basis of hormonal influences on the trigeminovascular system. In the present study we investigated the effect of physiological levels (10(-9) m) oestrogen on female rat trigeminal ganglia in vitro. Immunocytochemical analysis demonstrated the presence of oestrogen receptor-alpha in a predominantly cytoplasmic location and in neurites. Microarray analysis demonstrated that oestrogen treatment regulates several genes with potential relevance to menstrual migraine. The genes that were upregulated included synapsin-2, endothelin receptor type B, activity and neurotransmitter-induced early gene 7 (ania-7), phosphoserine aminotransferase, MHC-1b, and ERK-1. Down-regulated genes included IL-R1, bradykinin B2 receptor, N-tropomodulin, CCL20, GABA transporter protein, fetal intestinal lactase-phlorizin hydrolase, carcinoembryonic antigen-related protein, zinc finger protein 36, epsin 1 and cysteine string protein. Protein activity assays demonstrated that exposure of the cultured neurons to oestrogen leads to activation of ERK, which has been linked to inflammatory pain. Immunocytochemistry demonstrated that activated ERK was present in neurons containing peripherin, a marker of nociceptive neurons. Several of the genes in the present study may provide potential targets for understanding the association of oestrogen with migraine and other hormone-related orofacial pain.

Down beat nystagmus in vitamin B 12 deficiency syndrome

A 34 years old male, presenting with progressive proximal weakness, with a neurogenic pattern on needle EMG, and a family history suggestive of an autosomal recessive disorder, was found to have additional features of myeloneuropathy and a down beat nystagmus. A low serum vitamin B12 level was found, and on vitamin B12 supplementation there was a partial clinical as well as electrophysiological recovery.

Fine mapping of a susceptibility locus for bipolar and genetically related unipolar affective disorders, to a region containing the C21ORF29 and TRPM2 genes on chromosome 21q22.3

Linkage analyses of bipolar families have confirmed that there is a susceptibility locus near the telomere on chromosome 21q. To fine map this locus we carried out tests of allelic association using 30 genetic markers near the telomere at 21q22.3 in 600 bipolar research subjects and 450 ancestrally matched supernormal control subjects. We found significant allelic association with the microsatellite markers D21S171 (P=0.016) and two closely linked single-nucleotide polymorphisms, rs1556314 (P=0.008) and rs1785467 (P=0.025). A test of association with a three locus haplotype across the susceptibility region was significant with a permutation test of P=0.011. A two SNP haplotype was also significantly associated with bipolar disorder (P=0.01). Only two brain expressed genes, TRPM2 and C21ORF29 (TSPEAR), are present in the associated region. TRPM2 encodes a calcium channel receptor and TSPEAR encodes a peptide with repeats associated with epilepsy in the mouse. DNA from subjects who had inherited the associated marker alleles was sequenced. A base pair change (rs1556314) in exon 11 of TRPM2, which caused a change from an aspartic acid to a glutamic acid at peptide position 543 was found. This SNP showed the strongest association with bipolar disorder (P=0.008). Deletion of exon 11 of TRPM2 is known to cause dysregulation of cellular calcium homeostasis in response to oxidative stress. A second nonconservative change from arginine to cysteine at position 755 in TRPM2 (ss48297761) was also detected. A third nonconservative change from histidine to glutamic acid was found in exon 8 of TSPEAR. These changes need further investigation to establish any aetiological role in bipolar disorder.

SNP500Cancer: a public resource for sequence validation, assay development, and frequency analysis for genetic variation in candidate genes

The SNP500Cancer database provides sequence and genotype assay information for candidate SNPs useful in mapping complex diseases, such as cancer. The database is an integral component of the NCI Cancer Genome Anatomy Project (http://cgap.nci.nih.gov). SNP500Cancer reports sequence analysis of anonymized control DNA samples (n = 102 Coriell samples representing four self-described ethnic groups: African/African-American, Caucasian, Hispanic and Pacific Rim). The website is searchable by gene, chromosome, gene ontology pathway, dbSNP ID and SNP500Cancer SNP ID. As of October 2005, the database contains >13 400 SNPs, 9124 of which have been sequenced in the SNP500Cancer population. For each analysed SNP, gene location and >200 bp of surrounding annotated sequence (including nearby SNPs) are provided, with frequency information in total and per subpopulation as well as calculation of Hardy-Weinberg equilibrium for each subpopulation. The website provides the conditions for validated sequencing and genotyping assays, as well as genotype results for the 102 samples, in both viewable and downloadable formats. A subset of sequence validated SNPs with minor allele frequency >5% are entered into a high-throughput pipeline for genotyping analysis to determine concordance for the same 102 samples. In addition, the results of genotype analysis for select validated SNP assays (defined as 100% concordance between sequence analysis and genotype results) are posted for an additional 280 samples drawn from the Human Diversity Panel (HDP). SNP500Cancer provides an invaluable resource for investigators to select SNPs for analysis, design genotyping assays using validated sequence data, choose selected assays already validated on one or more genotyping platforms, and select reference standards for genotyping assays. The SNP500Cancer database is freely accessible via the web page at http://snp500cancer.nci.nih.gov.

Vitamin B12 deficiency: a clinical and electrophysiological profile

OBJECTIVE

The present study was conducted to evaluate the clinical and electrophysiological profile of vitamin B12 deficiency syndrome and whether a correlation exists between the disease process and the various electrophysiological parameters.

METHODS

40 patients with vitamin B12 deficiency neurological syndromes with low serum vitamin B12 and high homocysteine levels were subjected to a detailed motor and sensory nerve conduction studies and pattern reversal VER (P100), SSEP (P37) after stimulation of the posterior tibial nerve and median nerve (N 20) were obtained bilaterally. MR cervical spine was done in all the patients and MR brain in those who presented with neuro-psychiatric symptoms. The patients were followed up at three months, six months and one year after treatment.

RESULTS

On the basis of clinico-electrophysiological profile, 31 patients had myeloneuropathy, 5 isolated myelopathy, 4 isolated neuropathy. Four of the patients with myeloneuropathy, had concomitant dementia. MR imaging revealed abnormality in 12.5% of cases. Prolongation of P37 latency was observed in 39 (97.5%) patients, N 20 latency in 22 (55%), and P100 latency in 19 (47.5%) patients. Peripheral neuropathy was seen in 18 patients; optic neuropathy in 8; and combination of peripheral and optic neuropathy in 9 patients. The peripheral neuropathy was axonal in 19, and demyelinating in 6 patients. There was a significant correlation of the duration of the disease with N 20 latency (P < 0.04). Serum vitamin B12 level correlated well with the latencies of P37 (P < 0.005) and sural SNAP (P < 0.006). On treatment, normalization of P100, MRI signal, N 20 and partial recovery of P37 latencies was seen at 6 months, 9 months and one year respectively.

CONCLUSION

Differential recovery of central and peripheral syndromes was seen. This correlated with the underlying demyelinating and axonal processes, which was well reflected by the electrophysiological studies, and has an important bearing on the outcome.

Hiatal hernia recurrence: 2004

BACKGROUND

The incidence of laparoscopic hiatal hernia recurrence is less than ideal. The reasons are more theoretical than objective, as the literature has little data in support of specific mechanisms of recurrence.

METHOD

A recent literature review using all Internet-available, English-language articles on laparoscopic hernia repair was completed.

RESULTS

A multitude of mechanisms of recurrence are suggested, but only surgeon inexperience, postoperative vomiting, heavy lifting, and retention of the hernia sac are supported by data.

CONCLUSION

The incidence of hiatal hernia recurrence has stabilized. The role of an onlay mesh prosthesis for the prevention of hiatal hernia recurrence is under investigation, and long-term results are awaited.

In Vitro–In Vivo Characterization of Release Modifying Agents for Parenteral Sustained‐Release Ketorolac Formulation

One of the prerequisites for a parenteral preparation is that the excipients incorporated are biocompatible and biodegradable. In the present study hydrophilic and hydrophobic excipients were investigated for developing an intramuscular sustained-release formulation of ketorolac. Kollidon 17 PF, Peceol (glyceryl monooleate), and castor oil were chosen as the potential release-retarding agents, each with a distinct mechanism of action. They were evaluated by in vitro drug-release profiles and in vivo pharmacodynamic and pharmacokinetic study in mice. Cumulative drug release was determined for standard and test formulations in modified Franz diffusion cell. Pharmacodynamic parameter, T = 70% response of peak analgesic response, was used to compare the performance of test formulations. Based on pharmacodynamic/pharmacokinetic correlation in the animal studies, Css(max) and Css(min) of 51.39 and 30.0 microg/mL, respectively, were determined and considered as performance markers for pharmacokinetic evaluation of test formulations. The study suggested that the sustained-release capability of glyceryl monooleate was maximum followed by that of castor oil and Kollidon 17 PF, when compared to conventional ketorolac tromethamine formulation. It was inferred that water soluble excipient, though, showed release retarding property in vitro but could not maintain it in the in vivo environment. Glyceryl monooloeate-based formulation produced the most favorable drug blood concentration vs. time profile.

Brachial plexopathy: a clinical and electrophysiological study

BACKGROUND

A retrospective study to evaluate the clinical and electrophysiological profile of brachial plexus lesions in a tertiary care center of India.

METHODS

Thirty eight patients with brachial plexopathy (idiopathic or traumatic) with detailed electrophysiological studies were sampled. This included detailed motor and sensory nerve conduction studies of the conventional median, ulnar and radial nerves of the upper limbs, CMAP from deltoid, biceps and triceps on stimulating the ERB's point, needle EMG in the appropriate muscles and paraspinal muscles. The electrophysiological studies were performed on both sides irrespective of the clinical involvement and were recorded within 1.61 +/- 2.89 months in idiopathic group and 2.11 +/- 2.65 months in traumatic plexopathy group. The severity of involvement was assessed on MRC scale. ADL scale was used to assess the disability at presentation and subsequent follow up.

RESULTS

12 patients (11 male and 01 female) had idiopathic brachial plexopathy and 26 patients (all male) had traumatic brachial plexopathy. In the idiopathic group the lesion was localized to upper trunk in 58.3% of patients and middle trunk (posterior cord) in 41.66% and none had lower trunk or diffuse involvement. 25% had bilateral involvement. Two patients (16.6%) with idiopathic plexitis had recurrence involving the opposite side during the follow up. In the traumatic group the lesion was localized to the upper trunk in 11.53%, middle trunk (posterior cord) in 57.69% and 30.76% of patients had diffuse involvement. All the patients in traumatic plexopathy group had severe disability while in idiopathic group 91.66% had severe disability and 8.33% had moderate disability. Low amplitude CMAP and F wave abnormality were seen in 16.6% of patients in idiopathic group. On needle EMG 83.3% had fasciculation or fibrillations while none had paraspinal EMG abnormality. In traumatic group low to absent CMAP was seen in 69.2% and 76.92% had F wave abnormality. SNAPs were not recordable in 53.8%. On Needle EMG all the patients showed fasciculation or fibrillations and only 6 (23.0%) had paraspinal muscle fibrillations. Root avulsion could be documented in only four of these cases on MR imaging.

CONCLUSIONS

Recovery in the traumatic group correlated well with the electrophysiological abnormalities while no such correlation was evident in the idiopathic group.

Paroxysmal kinesigenic dyskinesia manifestation of hyperthyroidism

Sporadic paroxysmal kinesigenic dyskinesia (PKD) secondary to thyrotoxicosis is an extremely rare entity. A 36-year-old female presented with the features of PKD. Her investigations revealed thyrotoxicosis. Her dyskinesia did not respond to carbamazepine but remitted with the anti-thyroid drug, neomercazole. Perhaps hyperthyroidism-related PKD is a result of a metabolic disturbance of the basal ganglia circuits rather than a permanent and irreversible change.

Effect of losartan on albuminuria, peripheral and autonomic neuropathy in normotensive microalbuminuric type 2 diabetics

BACKGROUND

Angiotensin converting enzyme (ACE) inhibitors are emerging as effective agents for preventing microvascular complications of diabetes. Losartan (angiotensin II antagonist) has an antihypertensive efficacy equivalent to ACE inhibitors, however its role in microvascular complications is not yet known.

MATERIAL AND METHODS

We studied the efficacy of losartan (50 mg once daily for 12 weeks) on albuminuria, peripheral and autonomic neuropathy in 25 normotensive microalbuminuric type 2 diabetics who were asymptomatic for neuropathy.

RESULTS

Mean age was 46.6 +/- 4.34 years with the average duration of diabetes being 8.1 +/- 1.54 years. Albuminuria improved significantly from 54 +/- 9.35 mg/L to 32.8 +/- 25 mg/L (Paired student's t-test, P=0.0005) after therapy. Autonomic neuropathy was observed in 64% while 76% had peripheral neuropathy; but there was no improvement with losartan. The duration of diabetes had a negative correlation with autonomic neuropathy. It also had a similar negative correlation with median and common peroneal nerve motor conduction velocities (Pearson's correlation coefficient, r = -0.53, P<0.01 and r = -0.56, P<0.01 respectively) implying that autonomic and peripheral neuropathy worsen as a diabetic ages. However, no correlation existed between albuminuria and autonomic or peripheral nerve function.

CONCLUSION

Autonomic and peripheral neuropathy are highly prevalent in normotensive microalbuminuric diabetic patients. Losartan remarkably improves albuminuria but a similar benefit in autonomic or peripheral neuropathy is not seen over 12 weeks. The future may see a defining role for losartan in microvascular complications in normotensive diabetics.

Effects of electron-beam irradiation on buccal-cell DNA

Buccal cells were collected from 29 participants, by use of mouthwash rinses, and were split into equal aliquots, with one aliquot irradiated by electron-beam (E-beam) irradiation equivalent to the sterilizing dosage used by the U.S. Postal Service and the other left untreated. Aliquots were extracted and tested for DNA yields (e.g., TaqMan assay for quantifying human genomic DNA), genomic integrity, and amplification-based analysis of genetic variants (e.g., single-nucleotide polymorphisms [SNPs] and single tandem repeats [STRs]). Irradiated aliquots had lower median DNA yields (3.7 microg/aliquot) than untreated aliquots (7.6 microg/aliquot) (P<.0005) and were more likely to have smaller maximum DNA fragment size, on the basis of genomic integrity gels, than untreated aliquots (P<.0005). Irradiated aliquots showed poorer PCR amplification of a 989-bp beta-globin target (97% for weak amplification and 3% for no amplification) than untreated aliquots (7% for weak amplification and 0% for no amplification) (P<.0005), but 536-bp and 268-bp beta-globin targets were amplified from all aliquots. There was no detectable irradiation effect on SNP assays, but there was a significant trend for decreased detection of longer STRs (P=.01) in irradiated versus untreated aliquots. We conclude that E-beam irradiation reduced the yield and quality of buccal-cell specimens, and, although irradiated buccal-cell specimens may retain sufficient DNA integrity for some amplified analyses of many common genomic targets, assays that target longer DNA fragments (>989 bp) or require whole-genome amplification may be compromised.