Modified SureSelectQXT Target Enrichment Protocol for Illumina Multiplexed Sequencing of FFPE Samples

Background

Personalised medicine is nowadays a major objective in oncology. Molecular characterization of tumours through NGS offers the possibility to find possible therapeutic targets in a time- and cost-effective way. However, the low quality and complexity of FFPE DNA samples bring a series of disadvantages for massive parallel sequencing techniques compared to high-quality DNA samples (from blood cells, cell cultures, etc.).

Results

We performed several experiments to understand the behaviour of FFPE DNA samples during the construction of SureSelect^QXT libraries. First, we designed a quality checkpoint for FFPE DNA samples based on the quantification of their amplification capability (qcPCR). We observed that FFPE DNA samples can be classified according to DIN value and qcPCR concentration into unusable, or low-quality (LQ) and good-quality (GQ) DNA. For GQ samples, we increased the amount of input DNA to 150 ng and the digestion time to 30 min, whereas for LQ samples, we used 50 ng of DNA as input but we decreased the digestion time to 1 min. In all cases, we increased the cycles of the pre-hyb PCR to 10 but decreased the cycles of the post-hyb PCR to 8. In addition, we confirmed that using half of the volume of reagents can be beneficial. Finally, in order to obtain better results, we designed a decision flow-chart to achieve a seeding concentration of 12–14 pM for MiSeq Reagent Kit v2.

Conclusions

Our experiments allowed us to unveil the behaviour of low-quality FFPE DNA samples during the construction of SureSelect^QXT libraries. Sequencing results showed that, using our modified SureSelect^QXT protocol, the final percentage of usable reads for low-quality samples was increased more than three times allowing to reach median depth/million reads values of 76.35. This value is equivalent to ~ 0.9 and ~ 0.7 of the values obtained for good-quality FFPE and high-quality DNA respectively.

Electronic supplementary material

The online version of this article (10.1186/s12575-018-0084-7) contains supplementary material, which is available to authorized users.

Helicobacter pylori second-line rescue therapy with levofloxacin- and bismuth-containing quadruple therapy, after failure of standard triple or non-bismuth quadruple treatments

BACKGROUND

The most commonly used second-line Helicobacter pylori eradication regimens are bismuth-containing quadruple therapy and levofloxacin-containing triple therapy, both offering suboptimal results. Combining bismuth and levofloxacin may enhance the efficacy of rescue eradication regimens.

AIMS

To evaluate the efficacy and tolerability of a second-line quadruple regimen containing levofloxacin and bismuth in patients whose previous H. pylori eradication treatment failed.

METHODS

This was a prospective multicenter study including patients in whom a standard triple therapy (PPI-clarithromycin-amoxicillin) or a non-bismuth quadruple therapy (PPI-clarithromycin-amoxicillin-metronidazole, either sequential or concomitant) had failed. Esomeprazole (40 mg b.d.), amoxicillin (1 g b.d.), levofloxacin (500 mg o.d.) and bismuth (240 mg b.d.) was prescribed for 14 days. Eradication was confirmed by (13) C-urea breath test. Compliance was determined through questioning and recovery of empty medication envelopes. Incidence of adverse effects was evaluated by questionnaires.

RESULTS

200 patients were included consecutively (mean age 47 years, 67% women, 13% ulcer). Previous failed therapy included: standard clarithromycin triple therapy (131 patients), sequential (32) and concomitant (37). A total of 96% took all medications correctly. Per-protocol and intention-to-treat eradication rates were 91.1% (95%CI = 87-95%) and 90% (95%CI = 86-94%). Cure rates were similar regardless of previous (failed) treatment or country of origin. Adverse effects were reported in 46% of patients, most commonly nausea (17%) and diarrhoea (16%); 3% were intense but none was serious.

CONCLUSIONS

Fourteen-day bismuth- and levofloxacin-containing quadruple therapy is an effective (≥90% cure rate), simple and safe second-line strategy in patients whose previous standard triple or non-bismuth quadruple (sequential or concomitant) therapies have failed.

Supporting medical planning by mitigating cognitive load

OBJECTIVES

Developing a care plan for a patient is a complex task, requiring an understanding of interactions and dependencies between procedures and of their possible outcomes for an individual patient. Decision support for planning has broader requirements than are typically considered in medical informatics applications. We consider the appropriate design of software to assist medical planning.

METHODS

The likely cognitive loads imposed by planning tasks were assessed with a view to directly supporting these via software.

RESULTS

Five types of cognitive load are likely to be important. A planning support system, REACT, was designed to ameliorate these cognitive loads by providing targeted dynamic feedback during planning. An initial evaluation study in genetic counselling indicates that the approach is successful in that role.

CONCLUSIONS

The approach provides the basis of a general aid for visualizing, customizing and evaluating care plans.

Cerebrospinal fluid leucocyte counts in healthy neonates

OBJECTIVES

To determine the cerebrospinal fluid (CSF) white blood cell (WBC) count of normal term neonates, and compare the CSF WBC profile of normal and symptomatic infants without infection of the central nervous system (CNS).

METHOD

Neonates were included if (a) they were at risk of congenital Toxoplasma infection and had undergone a lumbar puncture to assess CNS involvement, and (b) serial specific serum IgG and IgM determinations had ruled out congenital infection. According to neonatal chart reviews, 30 consecutive patients without CNS infection were classified as normal (absolutely asymptomatic) or symptomatic (any kind of symptoms).

RESULTS

CSF WBC count was higher in 11 symptomatic (7/mm(3), 0-30/mm(3)) than in 19 normal (1/mm(3), 0-5/mm(3)) neonates (p<0.01).

CONCLUSION

Normal neonatal CSF contains up to 5 WBCs/mm(3). Mild pleocytosis can be found in symptomatic infants without CNS infection.

Effect of octreotide on small intestinal motility in HIV-infected patients with chronic refractory diarrhea

Octreotide has been used to treat HIV-associated diarrhea. We aimed to assess the effect of octreotide on small intestinal motility in a group of HIV infected individuals with chronic diarrhea. Small intestinal motility was measured continuously for 48 hr by ambulatory strain gauge manometry in 12 HIV seropositive subjects with chronic diarrhea. During the second 24-hr period, intravenous octreotide was administered (100 microg every 8 hr). Postprandial and nocturnal fasting motility data were compared before and during administration of octreotide. Octreotide was associated with increased numbers of migrating motor complexes (MMCs) (7.25 vs 4.92, P = 0.03), and a relative decrease in the duration of phase II (22% vs 49.8, P = 0.03) during nocturnal fasting activity. Postprandial activity was absent in half of the subjects and the duration significantly reduced in the remainder. In conclusion, octreotide has a significant effect on small intestinal motility in HIV-infected individuals with diarrhea, which may influence intestinal transit.

Complications of central venous catheters in patients with haemophilia and inhibitors

We report our clinical experience with central venous catheters (CVCs) in 15 patients with haemophilia who, in total, had 34 catheters inserted. Eighteen devices were Hickman, six were Port-A-Cath and 10 were nontunnelled catheters (one Quinton, seven antecubital, one jugular and one subclavian vein access). All patients had factor VIII/IX inhibitors at the time of insertion. The mean age at operation was 8.8 years (range 16 months-39 years). Eight of the 15 patients (26/34 implanted catheters, 76%) presented some kind of complication. Pericatheter bleeding during the postoperative period affected a total of seven CVCs (7/34, 20%) in six patients, which required substitutive treatment for several days. Infection was reported in 15 of the CVCs (15/34, 44%), and four of these (4/15, 26%) had more than one episode, with a mean of 1.4 infection episodes per catheter (21/15). The infection rate was 0.2 infections per 1000 patient days or 0.1 per 1000 catheter days. Despite the usefulness of CVCs in haemophilic patients, the high incidence of complications requires careful assessment of the type of device as well as continuous surveillance.

The measurement of forces exerted during colonoscopy

BACKGROUND

The widely varying forces used at colonoscopy have not been measured. An electronic device was designed to measure the forces exerted by the clinician on the endoscope during colonoscopy.

METHODS

The device featured a handle designed in the shape of a hinged split cylinder that could be locked around the endoscope but readily moved up and down the insertion tube as the colonoscopy proceeded. This cylinder contained strain-gauges arranged so that the forces transmitted could be accurately measured. The device recorded the torque forces in addition to the push and pull forces exerted during diagnostic colonoscopy.

RESULTS

In a series of 21 colonoscopies in 20 patients: peak pushing force = 4.4 kg, pulling force = -1.8 kg, anti-clockwise torque = 1.0 Newton meters, clockwise torque = 0.8 Newton meters. Percentage time force greater than 1 kg = 5%. Peak anal insertion force = 1.8 kg.

CONCLUSIONS

These measurements represent the first accurate measurements of the forces exerted during colonoscopy. Reducing the force during colonoscopy is likely to diminish pain and reduce the risk of perforation. A knowledge of these forces may also help with the design of new instruments and models for teaching or research.

Human small bowel motor activity in response to liquid meals of different caloric value and different chemical composition

Previous animal studies have shown that the nature and duration of postprandial motility in the small bowel depend both on the caloric load and the chemical composition of a meal. It is not clear whether this is also true for the human small bowel. Therefore we investigated the motor activity of the human small bowel in response to nutrient liquids of different caloric value and different chemical composition. Ten human volunteers underwent three separate, 24-hr ambulatory manometry studies. They drank water, a pure glucose solution, and Intralipid 10% in volumes of both 300 and 600 ml. The caloric value of the nutrient liquids was 330 and 660 kcal, respectively. Records were analyzed visually for the reappearance of phase III of the MMC after ingestion of a test liquid, and a validated computer program calculated the incidence and amplitude of contractions during the postprandial period. Neither duration of the postprandial interval nor the mean incidence or mean amplitude of contractions were different between the fat and the carbohydrate solutions, but phase III reappeared significantly later after ingestion of the nutrient liquids than after water (P = 0.0002). Duration of the postprandial interval also depended on the volume or the caloric load of a liquid meal (P = 0.0012). Mean incidence of contractions tended to be higher after ingestion of nutrient liquids than after water (P = 0.059). We conclude that in ambulant subjects, small bowel motor activity in response to chemically diverse liquid meals is remarkably uniform. This is true for the duration of the postprandial motor activity, as well as the incidence and amplitude of contractions during that period. The caloric value of a liquid meal, however, regulates the duration of the postprandial interval in the human small bowel.

Acute otitis media in childhood: a study of 20,532 cases

We present a study of acute otitis media among 20,532 Spanish children during a 6-month period from January through June 1991. The study was done by distributing a questionnaire to all Spanish pediatricians. Of the patients 51.7% were girls and 48.3% boys; 68.7% of all children were younger than 5 years. The most frequent symptoms were otalgia or irritability, 92.7%; fever, 63.5%; otorrhea, 24.9%; vomiting, 21.4%; and another concomitant upper respiratory tract infection, 65.5%. Otitis was bilateral in 45.6% of the cases. The most frequently used antibiotic was cefixime (38%), followed by amoxicillin-clavulanate (22.2%), amoxicillin (15.3%), 2nd-generation cephalosporins (13.5%) and macrolides (8.8%). In 11.8% of the patients, a change in the initial antibiotic therapy was required due to adverse effects. Resolution of symptoms occurred in 77.8% of the patients.

Small bowel motility following major intra-abdominal surgery: the effects of opiates and rectal cisapride

BACKGROUND/AIMS

Human small bowel motility is altered after laparotomy. Opiate analgesia is a possible cause of these alterations, and cisapride is a potential therapy.

METHODS

Continuous proximal small bowel manometry was performed for up to 92 hours in 23 patients after major intra-abdominal surgery. They were treated with rectal cisapride (30 mg three times daily) or placebo until the clinical resolution of ileus. Small bowel manometry was performed for 30 hours in 5 volunteers receiving 1 mg/kg meperidine over 3 hours.

RESULTS

Phase III activity was present within 3 hours of the end of surgery in all patients. Initially, the migrating motor complex (MMC) period was markedly reduced (mean, 22 minutes) but gradually increased. Phase II activity was absent until a median of 40 hours had elapsed. Phase III contractile amplitude was markedly attenuated in the jejunum, in contrast to that in the duodenum, presumably as a result of dilatation and/or altered tone, increasing to normal by 72 hours. In the volunteer group, although the MMC period was reduced by meperidine, it remained significantly greater than that of the placebo patient group for approximately 48 hours and phase II was reduced but not eliminated. Cisapride induced some changes in motor activity but did not accelerate the recovery of normal motility. Clinical outcome, assessed by the return of bowel sounds and passage of flatus, was accelerated by cisapride, but the trend was not significant (P = 0.11).

CONCLUSIONS

This is the first published study using prolonged manometry to show the gradual evolution of small bowel motor activity after major intra-abdominal surgery. The findings suggest that surgery decreases the MMC period to the equivalent of the absolute refractory period, thereby eliminating phase II, which returns as the MMC period lengthens. Cisapride, at the dosage given, confers only modest benefit.

Mononucleosis caused by Epstein-Barr virus and cytomegalovirus in children: a comparative study of 124 cases

We present 124 children who had mononucleosis. The patients were selected according to strict clinical features. Twenty (16.1%) of the 124 children were proved to have cytomegalovirus mononucleosis and 104 (83.8%) children had Epstein-Barr virus mononucleosis. The symptoms were similar in both groups. Significant differences were found only for the presence of cervical lymphadenopathy, which was more frequent in the Epstein-Barr group (83.2%) compared with the cytomegalovirus group (75%). Fever was the most frequent symptom in both groups. Cytomegalovirus mononucleosis was significantly more frequent in children younger than 4 years.

Daytime ingestion of alcohol alters nighttime jejunal motility in man

We studied the effects of acute ingestion of intoxicating doses of alcohol on jejunal motility in six male volunteers ages 24-45 who had two 24-hr ambulatory manometries, one week apart, that each included three standardized meals with either red wine (0.6 g of alcohol/kg) or dealcoholized wine. Breath alcohol was measured at regular intervals for 3 hr following alcohol. The results show that the MMC cycle was significantly (P < 0.01) shorter during the night than during the day in the "nonalcohol" group but not in the "alcohol" group and that the amplitude of contractions was higher during the night than the day in the alcohol group (P < 0.01). All meals interrupted the MMC and induced a fed pattern. After the 300-kcal liquid meal, the duration of the fed pattern was shorter (P < 0.01), with a lower motility index (P < 0.01) and fewer contractions (P < 0.01), than following the two 600-kcal meals. The number of clustered contractions occurring in the postprandial period was lower in the alcohol group than in the nonalcohol group. After the three alcohol doses, a breath alcohol peak was reached in 20-60 min, and in all subjects, breath alcohol fell below 22 micrograms/100 ml after the third hour. This study showed that alcohol had only minor effects on postprandial contractile activity but abolished the circadian variation of the MMC normally seen in healthy subjects. The fact that breath alcohol was low by the time of onset of sleep, suggests that the effects on the MMC may be mediated through central rather than local mechanisms.

The computer as referee in the analysis of human small bowel motility

The aim of this study was to determine whether visual analysis of graphic records of small bowel motility is a reliable method of discriminating pressure events caused by bowel wall contraction from those of extraenteric origin and to compare this method with computerized analysis. Each of six independent observers was supplied with the same pair of records of 1 h of fasting diurnal duodenojejunal motility, acquired with a 3-channel ambulant data-logging system; one record included many artifacts due to body movement while the other did not. The observers were asked to identify and classify pressure events and to measure the duration and amplitude of "true" contractions. A computer program for on-line analysis is described; the algorithm was designed to overcome the problems of a variable baseline and sudden changes in pressure due to body movements that are unavoidable in prolonged recording from the small bowel of ambulant subjects. For regular contractions (phase III of migrating motor complex) there was good agreement between observers but not for irregular contractions, particularly when movement artifacts were abundant. When the observers were asked to repeat the analysis 6 mo later, there was poor agreement with their original identification of irregular contractions and artifacts. There was, however, good agreement between the computer analysis, which was totally reproducible, and the median decisions of the observer group; this agreement supports the validity of our computer algorithm. We conclude that computer analysis is not merely a valuable ergonomic aid for analysis of large quantity of data acquired in prolonged ambulatory monitoring, but also that, even for brief recordings, it provides a standard of reproducibility unmatched by "expert" inspection. Visual analysis is unreliable and thus susceptible to subjective bias; this may, in part, account for conflicting reports of small bowel motility under similar conditions reported by different workers in our own and other laboratories.

Assessment by prolonged ambulatory manometry of the effect of oral cisapride on proximal small bowel inter-digestive motility

The effects of cisapride, given orally at standard therapeutic dosage (10 mg tds), on proximal small bowel interdigestive motility in ten healthy volunteers was assessed by prolonged ambulatory manometry. Cisapride did not alter the duration of the MMC cycle, duration of phase II or the propagation rate of phase III in either the daytime or nighttime periods. However, when compared to studies, in which subjects received no drug, both nighttime and daytime phase II mean contractile amplitude, but not contractile incidence, were significantly increased (P < or = 0.001) by cisapride. Cisapride significantly increased the incidence of distally propagated clustered activity. We conclude that the major effects of cisapride on healthy small bowel motor function is to increase the mean contractile amplitude and incidence of distally propagated clustered activity.

Phalangeal osteoid osteoma in the hand

Three examples of osteoid osteoma of the phalanges have presented in our clinic in one year. The pain was the most significant clinical feature. The pain was either unrelieved or incompletely relieved by aspirin. Routine x-rays in the early stages of the disease were unhelpful in diagnosis. It is recommended that bone scanning is a useful diagnostic aid.