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- Jemt, Anders, 1985-, et al.
(författare)
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Evaluation of methods for whole genome and transcriptome sequencing from nanograms of FFPE samples
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Annan publikation (övrigt vetenskapligt/konstnärligt)abstract
- The most widely used method for the preservation of clinical tissue specimens is formalin fixation and paraffin embedding (FFPE). Simultaneous analysis of RNA and DNA from samples preserved using this method have long proved problematic, primarily due to lack of material. Here, we describe an attempt to build a complete analysis package for RNA and DNA extracted from single tissue sections. The workflow includes quality control of the extracted material, library preparation and data analysis. We extract DNA with varying integrity from FFPE sections and subject them to whole genome sequencing using two library preparation methods, Illumina TruSeq Nano using the Illumina NeoPrep and Rubicon Genomics ThruPlex. We are able to obtain some usable data, albeit with high duplication rates, demonstrating both the possibilities and challenges of sequencing damaged DNA. Two different approaches to transcriptome sequencing are assessed, the TruSeq RNA Access library preparation kit from Illumina and the SMARTer Stranded Total RNA-Seq Kit - Pico Input from Clonetech. The sequence capture approach of the TruSeq kit is shown to be more robust to low integrity RNA compared to the SMARTer kit. However, the SMARTer kit needs much less starting material and is able to yield data about all transcripts, not just protein coding mRNA.
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| 3. |
- Aschim, EL, et al.
(författare)
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Linkage between cryptorchidism, hypospadias, and GGN repeat length in the androgen receptor gene
- 2004
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Ingår i: Journal of Clinical Endocrinology and Metabolism. - : The Endocrine Society. - 1945-7197 .- 0021-972X. ; 89:10, s. 5105-5109
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Tidskriftsartikel (refereegranskat)abstract
- Although sufficient androgen receptor (AR) function is crucial for normal male sexual differentiation, single-point mutations in the AR gene are infrequent in the two most common male congenital malformations, hypospadias and cryptorchidism. Because polymorphic CAG and GGN segments regulate AR function, we investigated whether there was any association between these polymorphisms and mentioned malformations. Genotyping was performed by direct sequencing of DNA from patients diagnosed with hypospadias (n = 51) and cryptorchidism ( n = 23) and controls ( n = 210). The subjects with hypospadias were divided into subgroups of glanular, penile, and penoscrotal hypospadias. Median GGN lengths were significantly higher ( 24 vs. 23) among both subjects with cryptorchidism, compared with controls ( P = 0.001), and those with penile hypospadias, compared with either controls ( P = 0.003) or glanular and penoscrotal hypospadias combined ( P = 0.018). The frequency of cases with GGN 24 or more vs. GGN = 23, differed significantly among those with cryptorchidism (65/35%), compared with controls (31/54%) ( P = 0.012), and among subjects with penile hypospadias (69/31%), compared with either controls ( P = 0.035) or glanular or penoscrotal hypospadias combined (32/55%) ( P = 0.056). There were no significant differences in CAG lengths between the cases and controls. Our findings indicate an association between GGN length and the risk of cryptorchidism and penile hypospadias, both conditions considered consequences of low androgenicity.
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| 6. |
- Eberhard, Jakob, et al.
(författare)
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Impact of therapy and androgen receptor polymorphism on sperm concentration in men treated for testicular germ cell cancer: a longitudinal study.
- 2004
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Ingår i: Human Reproduction. - : Oxford University Press (OUP). - 0268-1161 .- 1460-2350. ; 19:6, s. 1418-1425
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Tidskriftsartikel (refereegranskat)abstract
- Abstract in Undetermined BACKGROUND: Testicular cancer (TC) patients have a high survival rate, and the question of post-therapy recovery of sperm production and its dependence on genetic predisposition is of major interest. METHODS: Ejaculates were obtained from 112 TC patients at one or more of the following time points: post-orchidectomy, or 6, 12, 24, 36 and 60 months post-therapy. The lengths of the androgen receptor (AR) function modulating CAG and GGN repeats in leukocyte DNA were also analysed. RESULTS: No significant decrease in sperm concentration was seen in men who received 1-2 cycles of adjuvant chemotherapy (ACT). Radiotherapy (RT) or more than two cycles of chemotherapy (HCT) caused an initial decline in sperm concentration, which returned to pre-treatment levels 2-5 years after therapy. In the HCT group, sperm concentration 12-24 months post-treatment (T(12-24)) was inversely correlated with CAG length (rho = -0.72, P = 0.03). The type of treatment, but not the concentration at T(0), was an independent predictor of sperm concentration at T(6) (P < 0.0005) and T(12-24) (P = 0.004). CONCLUSION: ACT did not induce a significant decline in sperm concentration. After HCT and RT, a significant reduction of sperm concentration was observed, recovering to pre-treatment levels 2-5 years post-treatment. In HCT-treated patients, the AR CAG length influenced the recovery of spermatogenesis.
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| 8. |
- Eriksson, Marie, et al.
(författare)
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Avloppsvatten : Rening av avloppsvatten i Sverige
- 2016
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Rapport (övrigt vetenskapligt/konstnärligt)abstract
- Utvecklingen de senaste 200 åren har gått från nedgrävda latriner via underjordiska kloaker som släpptes ut i närmaste sjö eller kustvatten till avancerade avloppsreningsverk. Avloppsfrågan har förändrats från att vara lösningen på ett lokalt sanitärt problem till att bli en global miljöfråga.Rening av avloppsvatten i Sverige ges ut av Naturvårdsverket och beskriver hur reningen av avloppsvatten från tätorter utvecklats i Sverige under 1900- och 2000-talen. Skriften ges ut vartannat år och har uppdaterats med senaste statistiken från 2014 angående utsläpp och slam från reningsverk.Informationen presenteras enligt artikel 16 i avloppsdirektivet (91/271/EEG). Direktivet omfattar allt avloppsvatten som samlas upp i ledningsnät, men kvantitativa krav ställs bara för de reningsverk som betjänar mer är 2 000 personer. I Sverige motsvarar det drygt 400 anläggningar. De gamla medlemsländerna i EU (EU15) skulle ha uppfyllt alla åtgärder inom ramen för direktivet vid utgången av 2005. De 12 nya EU-länderna har olika övergångsregler.
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