José A. Cocho

A glimpse into past, present, and future DNA sequencing.

Current advances in DNA sequencing technologies are dropping down sequencing cost while increasing throughput at a pace never shown before. Past-decade great milestones, as the establishment of a reference human genome (amongst others) and large-scale human genetic variation study in the 1000 Genome project are, in conjunction with the use of these techniques, triggering advances in many areas of basic and applied science. These tools, stored in and combined with the vast amount of information present in biological online databases are, with the use of automated interpretation and analysis tools, allowing the fulfillment of increasingly ambitious studies in many areas and also are democratizing the access to information, interpretation and technologies, being the first opportunity for researchers to assess the influence of genetics in complex events as multifactorial diseases, evolutionary studies, metagenomics, transcriptomics, etc. In this review, we present the current state of the art of these technologies, focusing on second generation sequencing, from sample and library preparation to sequencing chemistries and bioinformatic software available for final data analysis and visualisation, with its possible applications. We also make an overview of first and third generation, due to its historical importance and for being the upcoming future tools for genetic analysis, respectively.

Selenium speciation in cow milk obtained after supplementation with different selenium forms to the cow feed using liquid chromatography coupled with hydride generation-atomic fluorescence spectrometry

The purpose of this paper is to develop an easy and quick on-line selenium speciation method (LC-UV-HG-AFS) in cow milk obtained after different supplementation to cow feed. This study focuses on selenium speciation in cow milk after the use of different selenium species (organic selenium as selenised yeast and inorganic selenium as sodium selenite) in the supplementation of forages. Separation was carried out on a muBondapack C(18) column with the positively charged ion-pairing agent tetraethylammonium chloride in the mobile phase. The optimization of pre-reduction conditions was carried out; this step was done with UV irradiation and a heating block to improve the reduction of the different Se-compounds. Variables such as exposure time, hydrochloric acid concentration and temperature were studied. The detection limits for SeCyst(2), Se(IV), SeMet and Se(VI) were 0.4, 0.5, 0.9 and 1.0mugl(-1), respectively. The proposed method was applied to cow milk samples. The milk samples obtained after an organic supplementation of feeding as selenised yeast present three species of selenium, SeCyst2, Se(IV) and SeMet, while only SeCyst2 and Se(IV) are present in milk samples obtained after an inorganic supplementation of feeding.

Speciation of iron in breast milk and infant formulas whey by size exclusion chromatography-high performance liquid chromatography and electrothermal atomic absorption spectrometry.

Speciation of iron in milk was carried out by high performance liquid chromatography (HPLC) and electrothermal atomic absorption spectrometry (ETAAS). Milk whey was obtained and low molecular weight protein separation was performed by size exclusion chromatography (SEC) with a TSK Gel SW glass guard (Waters) pre-column and a TSK-Gel G2000 glass (Toso Haas) column. After studying water as a possible mobile phase, this mobile phase was carefully selected in order to avoid alterations of the sample and to make subsequent iron determination in the protein fractions easier by ETAAS. The proposed method is sensitive (limit of detection [LOD] and LOQ 1.4 and 4.7 microg l(-1), respectively) and precise (relative standard deviation [RSD]<10%). Iron is principally found in the proteins of 3 and 76 kDa in breast milk, and it is irregularly distributed in infant formulas.

Evaluation and long-term follow-up of infants with inborn errors of metabolism identified in an expanded screening programme.

Newborn screening (NBS) by tandem mass spectrometry started in Galicia (Spain) in 2000. We analyse the results of screening and clinical follow-up of inborn errors of metabolism (IEM) detected during 10 years. Our programme basically includes the disorders recommended by the American College of Medical Genetics. Since 2002, blood and urine samples have been collected from every newborn on the 3rd day of life; before then, samples were collected between the 5th and 8th days. Newborns who show abnormal results are referred to the clinical unit for diagnosis and treatment. In these 10 years, NBS has led directly to the identification of 137 IEM cases (one per 2060 newborns, if 35 cases of benign hyperphenylalaninemia are excluded). In addition, 33 false positive results and 10 cases of transitory elevation of biomarkers were identified (making the positive predictive rate 76.11%), and 4 false negative results. The use of urine samples contributed significantly to IEM detection in 44% of cases. Clinical symptoms appeared before positive screening results in nine patients (6.6%), four of them screened between days 5 and 8. The death rate was 2.92%; of the survivors, 95.5% were asymptomatic after a mean observation period of 54 months, and only two had an intellectual/psychomotor development score less than 85. Compared to other studies, a high incidence of type I glutaric aciduria was detected, one in 35,027 newborns. This report highlights the benefits of urine sample collection during screening, and it is the first study on expanded newborn screening results in Spain.

Electrospray ionization tandem mass spectrometry for the simultaneous determination of opiates and cocaine in human hair.

A fast and highly sensitive electrospray ionization tandem mass spectrometry (ESI-MS/MS) method has been developed for the simultaneous determination of morphine, 6-methylacetylmorphine (6-MAM), codeine, cocaine and benzoylecgonine (BZE) in hair from drug abusers. Pulverized hair samples were subjected to an optimized matrix solid phase dispersion (MSPD) procedure with alumina, followed by diluted hydrochloric acid elution on column solid-phase extraction (SPE) clean-up/pre-concentration. Alternatively, samples were also subjected to an optimized ultrasound assisted enzymatic hydrolysis (USEH) with Pronase E, followed by an off-line SPE clean up/pre-concentration procedure. Positive electrospray ionization and multiple reaction monitoring (MRM) with one precursor ion/product ion transition were used for the identification and quantification (deuterated analogues of each target as internal standards) of each analyte. The chromatographic pump and the autosampler were used for injecting the standards and the hair extracts (20 μL) as a flow injection analysis mode. The highest sensitivity was achieved when delivering the targets with an acetonitrile/water/formic acid (80/19.875/0.125) mixture. The limits of detection of the method were 39.2, 4.4, 6.8, 7.0 and 7.4 ng g(-1) for morphine, 6-MAM, codeine, cocaine and BZE, respectively. Relative standard deviations of intra- and inter-day precision were lower than 9 and 12%, respectively; whereas, analytical recoveries ranged from 96±5 to 106±4%. The developed method (MSPD-ESI-MS/MS) was applied to different hair samples from polydrug abusers, and results were statistically compared to those obtained after a conventional gas chromatography-mass spectrometry (GC-MS) analysis and also after USEH and ESI-MS/MS or GC-MS determinations.

Iron and zinc in hydrolised fractions of human milk and infant formulas using an in vitro method

Abstract The development of an in vitro method to simulate new-born digestion and to study iron and zinc bioavailability from human milk and cows milk based infant formulas was carried out. Enzyme treatment was conducted in two stages involving (1) pepsin at pH 5.0 followed by (2) pancreatin at neutral pH, where the incubation times were kept short to mimic the fast transit in the infants gastrointestinal tract. Solubility of trace elements was used to express bioavailability, and so analytes were determined in the fractions obtained after centrifugation by flame atomic absorption spectrometry (FAAS) using a high performance nebulizer. The results were compared to those obtained by performing gastric digestion at pH 2.0 for an adult, using various incubators to treat the sample and centrifugation or ultracentrifugation to separate soluble fractions. No differences in iron bioavailability from breast milk and infant formulas at different pHs could be detected due to the variability of the infant formulas analysed. However, zinc bioavailability from breast milk samples was higher than those obtained from infant formulas at the new born gastric pH.

Glutaric aciduria type I: Outcome of patients with early- versus late-diagnosis

Patients with Glutaric aciduria type 1 (GA-1) can be identified by newborn screening using tandem mass spectrometry. The clinical evolution of screened patients seems to be more favourable compared with those diagnosed later, although long-term evolution is still doubtful. We have evaluated the outcome in nine GA-1 patients diagnosed in our region during 12 years. Six were detected by newborn screening and 3 clinically. The birth prevalence was 1:35,027. High blood C5DC concentration, in 8/9 patients, was found, whereas all patients exhibited high concentration of this metabolite in urine. Therefore, urine C5DC was a good marker for the detection of this disease. Eight different mutations in the GCDH gene were identified, four of them were novel (p.R88H, p.Y398C, p.R372K, p.D220N); being p.R227P the mostcommon. Macrocephaly with enlarged frontotemporal subarachnoid space was present in 4/6 patients diagnosed by newborn screening, all these patients required high energy intake, and in two cases, enteral feeding during the first year of life was needed. One child had an intercurrent episode of feeding refuse with hypoglycemia at two years of age. The mean follow-up time of screened patients was 56 months, and patients still remain asymptomatic. However, after a mean follow-up of 97 months treatment efficacy was poor in unscreened patients, two of them showing a severe spastic tetraparesis. Plasma levels of lysine, tryptophan and carnitine, were the most useful biomarkers for the follow-up. Our data support that, early diagnosis and treatment strategies are essential measures for the good clinical evolution of GA-1 patients.

Assessment of a targeted resequencing assay as a support tool in the diagnosis of lysosomal storage disorders

BackgroundWith over 50 different disorders and a combined incidence of up to 1/3000 births, lysosomal storage diseases (LSDs) constitute a major public health problem and place an enormous burden on affected individuals and their families. Many factors make LSD diagnosis difficult, including phenotype and penetrance variability, shared signs and symptoms, and problems inherent to biochemical diagnosis. Developing a powerful diagnostic tool could mitigate the protracted diagnostic process for these families, lead to better outcomes for current and proposed therapies, and provide the basis for more appropriate genetic counseling.MethodsWe have designed a targeted resequencing assay for the simultaneous testing of 57 lysosomal genes, using in-solution capture as the enrichment method and two different sequencing platforms. A total of 84 patients with high to moderate-or low suspicion index for LSD were enrolled in different centers in Spain and Portugal, including 18 positive controls.ResultsWe correctly diagnosed 18 positive blinded controls, provided genetic diagnosis to 25 potential LSD patients, and ended with 18 diagnostic odysseys.ConclusionWe report the assessment of a next–generation-sequencing-based approach as an accessory tool in the diagnosis of LSDs, a group of disorders which have overlapping clinical profiles and genetic heterogeneity. We have also identified and quantified the strengths and limitations of next generation sequencing (NGS) technology applied to diagnosis.

Application of dispersive liquid-liquid microextraction for the determination of phosphatidylethanol in blood by liquid chromatography tandem mass spectrometry.

Phosphatidylethanol (PEth) is a phospholipid which requires for its metabolic formation the presence of relatively high ethanol levels. PEth is thus a promising marker to quentify ethanol abuse. Dispersive liquid-liquid microextraction has become a popular technique because it is fast, inexpensive, easy to operate and consumes low volume of organic solvent. In this method, the appropriate mixture of extraction solvent (230 μL dichloromethane) and disperser solvent (630 μL acetone) are injected into the sample by syringe, rapidly. The liquid chromatography method using a reversed phase-C8 column and a negative ion mode electrospray ionization tandem mass spectrometry detection instrument was developed for the determination of small amounts of PEth that might be present in blood samples, using phosphatidylbutanol (PBut) as an internal standard. The sensitivity of detection obtained with tandem MS was better than that of previous methods. Good linearity was obtained for a range of LOQ-10 μg/mL for PEth, whereas all of the deviations in precision and accuracy were less than 15% except for the LLOQ, where it should not exceed 20%. A set of 50 blood samples were analyzed by such method and whole blood concentrations of PEth 16:0/18:1 ranged from LLOQ to 1.71 μg/mL.

Direct tandem mass spectrometry for the simultaneous assay of opioids, cocaine and metabolites in dried urine spots

A micro-analytical method based on spotting urine samples (20μL) onto blood/urine spot collection cards followed by air-drying and extraction (dried urine spot, DUS) was developed and validated for the screening/confirmation assay of morphine, 6-methylacetylmorphine (6-MAM), codeine, cocaine and benzoylecgonine (BZE). Acetonitrile (3 mL) was found to be a useful solvent for target extraction from DUSs under an orbital-horizontal stirring at 180 rpm for 10 min. Determinations were performed by direct electrospray ionization tandem mass spectrometry (ESI-MS/MS) under positive electrospray ionization conditions, and by using multiple reaction monitoring (MRM) with one precursor ion/product ion transition for the identification and quantification (deuterated analogs of each target as internal standards) of each analyte. The limits of detection of the method were 0.26, 0.94, 1.5, 1.1, and 2.0 ng mL(-1), for cocaine, BZE, codeine, morphine and 6-MAM, respectively; whereas, relative standard deviations of intra- and inter-day precision were lower than 8 and 11%, respectively, and intra- and inter-day analytical recoveries ranged from 94±4 to 105±3%. The small volume of urine required (20 μL), combined with the simplicity of the analytical technique makes it a useful procedure for screening/quantifying drugs of abuse. The method was successfully applied to the analysis of urine from polydrug abusers.