Helgi J. Ísaksson

A Variant Associated with Nicotine Dependence, Lung Cancer and Peripheral Arterial Disease

Smoking is a leading cause of preventable death, causing about 5 million premature deaths worldwide each year. Evidence for genetic influence on smoking behaviour and nicotine dependence (ND) has prompted a search for susceptibility genes. Furthermore, assessing the impact of sequence variants on smoking-related diseases is important to public health. Smoking is the major risk factor for lung cancer (LC) and is one of the main risk factors for peripheral arterial disease (PAD). Here we identify a common variant in the nicotinic acetylcholine receptor gene cluster on chromosome 15q24 with an effect on smoking quantity, ND and the risk of two smoking-related diseases in populations of European descent. The variant has an effect on the number of cigarettes smoked per day in our sample of smokers. The same variant was associated with ND in a previous genome-wide association study that used low-quantity smokers as controls, and with a similar approach we observe a highly significant association with ND. A comparison of cases of LC and PAD with population controls each showed that the variant confers risk of LC and PAD. The findings provide a case study of a gene–environment interaction, highlighting the role of nicotine addiction in the pathology of other serious diseases.

A common variant associated with prostate cancer in European and African populations

With the increasing incidence of prostate cancer, identifying common genetic variants that confer risk of the disease is important. Here we report such a variant on chromosome 8q24, a region initially identified through a study of Icelandic families. Allele −8 of the microsatellite DG8S737 was associated with prostate cancer in three case-control series of European ancestry from Iceland, Sweden and the US. The estimated odds ratio (OR) of the allele is 1.62 (P = 2.7 × 10−11). About 19% of affected men and 13% of the general population carry at least one copy, yielding a population attributable risk (PAR) of ∼8%. The association was also replicated in an African American case-control group with a similar OR, in which 41% of affected individuals and 30% of the population are carriers. This leads to a greater estimated PAR (16%) that may contribute to higher incidence of prostate cancer in African American men than in men of European ancestry.

Sequence variants at the TERT-CLPTM1L locus associate with many cancer types

The common sequence variants that have recently been associated with cancer risk are particular to a single cancer type or at most two. Following up on our genome-wide scan of basal cell carcinoma, we found that rs401681[C] on chromosome 5p15.33 satisfied our threshold for genome-wide significance (OR = 1.25, P = 3.7 × 10−12). We tested rs401681 for association with 16 additional cancer types in over 30,000 cancer cases and 45,000 controls and found association with lung cancer (OR = 1.15, P = 7.2 × 10−8) and urinary bladder, prostate and cervix cancer (ORs = 1.07−1.31, all P < 4 × 10−4). However, rs401681[C] seems to confer protection against cutaneous melanoma (OR = 0.88, P = 8.0 × 10−4). Notably, most of these cancer types have a strong environmental component to their risk. Investigation of the region led us to rs2736098[A], which showed stronger association with some cancer types. However, neither variant could fully account for the association of the other. rs2736098 corresponds to A305A in the telomerase reverse transcriptase (TERT) protein and rs401681 is in an intron of the CLPTM1L gene.

Genome-wide association study identifies multiple susceptibility loci for pulmonary fibrosis

We performed a genome-wide association study of non-Hispanic, white individuals with fibrotic idiopathic interstitial pneumonias (IIPs; n = 1,616) and controls (n = 4,683), with follow-up replication analyses in 876 cases and 1,890 controls. We confirmed association with TERT at 5p15, MUC5B at 11p15 and the 3q26 region near TERC, and we identified seven newly associated loci (Pmeta = 2.4 × 10−8 to 1.1 × 10−19), including FAM13A (4q22), DSP (6p24), OBFC1 (10q24), ATP11A (13q34), DPP9 (19p13) and chromosomal regions 7q22 and 15q14-15. Our results suggest that genes involved in host defense, cell-cell adhesion and DNA repair contribute to risk of fibrotic IIPs.

Genetic correction of PSA values using sequence variants associated with PSA levels.

Sequence variants in the human genome are associated with serum levels of prostate-specific antigen. SNPping Away at Prostate Cancer Measuring prostate-specific antigen (PSA) in serum is the only diagnostic test for prostate cancer and is used as a screening tool for deciding whether to perform a biopsy. Yet, this diagnostic test is far from ideal, with more than a third of men with serum PSA levels of 10 ng/ml or greater having no evidence of prostate cancer at biopsy, and some men with very low PSA levels (less than the lower threshold of 2.5 ng/ml), who are not given a biopsy but yet end up having prostate cancer. The lack of specificity and sensitivity of the PSA test and the many confounding factors that influence the test result, including medications, inflammation, and, of course, genotype, have reduced the value of this screening tool. As with most cancers, early detection of prostate cancer leads to a greatly improved chance of survival, so improving the predictive accuracy of this test is of paramount importance. In an effort to investigate whether genome sequence variants can be used to make the PSA test more sensitive, Gudmundsson and colleagues have undertaken a genome-wide association study in 15,757 Icelandic men and 454 British men not yet diagnosed with prostate cancer to see whether they can tie sequence variants [single-nucleotide polymorphisms (SNPs)] to serum PSA levels. The authors identify six loci with SNPs that correlate with PSA levels. They then probed these data more deeply. They looked at these loci in 3834 men who underwent subsequent biopsy of the prostate and demonstrate that three of these loci (10q26, 12q24, and 19q13.33) are associated not only with higher PSA levels but also with a higher probability of a negative biopsy result. The authors suggest that this genotype information should be used to calculate a personalized “cutoff” value for serum PSA levels in each individual to improve the predictive accuracy of the test and to ensure that only men who need a prostate biopsy are subjected to this procedure. Measuring serum levels of the prostate-specific antigen (PSA) is the most common screening method for prostate cancer. However, PSA levels are affected by a number of factors apart from neoplasia. Notably, around 40% of the variability of PSA levels in the general population is accounted for by inherited factors, suggesting that it may be possible to improve both sensitivity and specificity by adjusting test results for genetic effects. To search for sequence variants that associate with PSA levels, we performed a genome-wide association study and follow-up analysis using PSA information from 15,757 Icelandic and 454 British men not diagnosed with prostate cancer. Overall, we detected a genome-wide significant association between PSA levels and single-nucleotide polymorphisms (SNPs) at six loci: 5p15.33 (rs2736098), 10q11 (rs10993994), 10q26 (rs10788160), 12q24 (rs11067228), 17q12 (rs4430796), and 19q13.33 [rs17632542 (KLK3: I179T)], each with Pcombined <3 × 10−10. Among 3834 men who underwent a biopsy of the prostate, the 10q26, 12q24, and 19q13.33 alleles that associate with high PSA levels are associated with higher probability of a negative biopsy (odds ratio between 1.15 and 1.27). Assessment of association between the six loci and prostate cancer risk in 5325 cases and 41,417 controls from Iceland, the Netherlands, Spain, Romania, and the United States showed that the SNPs at 10q26 and 12q24 were exclusively associated with PSA levels, whereas the other four loci also were associated with prostate cancer risk. We propose that a personalized PSA cutoff value, based on genotype, should be used when deciding to perform a prostate biopsy.

Diagnostic Surgical Lung Biopsies for Suspected Interstitial Lung Diseases: A Retrospective Study

BACKGROUND Current guidelines for interstitial lung disease support a surgical biopsy for optimal diagnosis and treatment, yet only a minority of patients undergo such biopsy. Our objectives were to address the properties of a surgical lung biopsy for suspected interstitial lung disease, the diagnostic yield of the procedure, and whether it resulted in changes in diagnosis and treatment. METHODS A retrospective nationwide study including 73 patients (mean age, 57.3 years; 58% males) who underwent a surgical lung biopsy for suspected interstitial disease in Iceland between 1986 and 2007 was conducted. Patient records and histologic specimens were reviewed. Before the surgical biopsy a transbronchial or computed tomography-guided biopsy had been performed in two thirds of the patients. RESULTS The complication rate for surgical lung biopsy was 16%, and 30-day operative mortality was 2.7%, both significantly higher in patients with preoperative respiratory failure. After the procedure, a definite histopathologic diagnosis was obtained in 81% of the patients. Usual interstitial pneumonia was the most common diagnosis (31%). The clinical diagnosis was changed for 73% of the patients, and in 53% of the patients the biopsy resulted in changes in treatment. CONCLUSIONS Surgical lung biopsy is a powerful tool for diagnosis of suspected interstitial lung disease. It results in a specific diagnosis for the majority of patients and changes in treatment for more than half. Operative morbidity and mortality are low but still significant, so patients should be carefully selected for the procedure, especially those with respiratory failure.

Epidemiology of organising pneumonia in Iceland

Background: Cryptogenic organising pneumonia (COP) has also been called idiopathic bronchiolitis obliterans organising pneumonia. In secondary organising pneumonia (SOP) the causes can be identified or it occurs in a characteristic clinical context. The aim of this study was to determine the incidence and epidemiological features of COP and SOP nationwide in Iceland over an extended period. Methods: A retrospective study of organising pneumonia (OP) in Iceland over 20 years was conducted and the epidemiology and survival were studied. All pathological reports of patients diagnosed with or suspected of having COP or SOP in the period 1984–2003 were identified and the pathology samples were re-evaluated using strict diagnostic criteria. Results: After re-evaluation, 104 patients fulfilled the diagnostic criteria for OP (58 COP and 46 SOP). The mean annual incidence of OP was 1.97/100 000 population (1.10/100 000 for COP and 0.87/100 000 for SOP). The mean age at diagnosis was 67 years with a wide age range. The most common causes of death were lung diseases other than OP, and only one patient died from OP. Patients with OP had a lower rate of survival than the general population, but there was no statistical difference between COP and SOP. Conclusions: The incidence of OP is higher than previously reported, suggesting that OP needs to be considered as a diagnosis more often than has been done in the past.

Adenocarcinoma of the vermiform appendix. A population study.

We report seven cases of adenocarcinoma of the vermiform appendix occurring in Iceland during 1974–1989. The patients ranged in age from 25–83 years, mean age 55.1 years. There were five males and two females. Five had mucinous adenocarcinoma, two had adenocarcinoma. Four patients presented with symptoms and signs of acute appendicitis and all had surgically resectable disease. Three of these patients were alive with no evidence of disease four months, two years and 15 years after presentation; one death of disease occurred seven years after ileocecal resection. In three cases, the clinical presentation was that of metastatic adenocarcinoma of unknown origin. Of these patients two were diagnosed at autopsy and one after appendectomy for perforated appendicitis. Survival in this group was six weeks, three months and twelve months, respectively. In none of our patients was the diagnosis made preoperatively and no tumors were found in appendices removed incidental to other intra‐abdominal operations. The incidence of adenocarcinoma of the vermiform appendix in Iceland during 1974–1989 was approximately 0.2 cases/100.000/year.

Genome-Wide Significant Association Between a Sequence Variant at 15q15.2 and Lung Cancer Risk

Genome-wide association studies (GWAS) have identified 3 genomic regions, at 15q24-25.1, 5p15.33, and 6p21.33, which associate with the risk of lung cancer. Large meta-analyses of GWA data have failed to find additional associations of genome-wide significance. In this study, we sought to confirm 7 variants with suggestive association to lung cancer (P < 10(-5)) in a recently published meta-analysis. In a GWA dataset of 1,447 lung cancer cases and 36,256 controls in Iceland, 3 correlated variants on 15q15.2 (rs504417, rs11853991, and rs748404) showed a significant association with lung cancer, whereas rs4254535 on 2p14, rs1530057 on 3p24.1, rs6438347 on 3q13.31, and rs1926203 on 10q23.31 did not. The most significant variant, rs748404, was genotyped in an additional 1,299 lung cancer cases and 4,102 controls from the Netherlands, Spain, and the United States and the results combined with published GWAS data. In this analysis, the T allele of rs748404 reached genome-wide significance (OR = 1.15, P = 1.1 × 10(-9)). Another variant at the same locus, rs12050604, showed association with lung cancer (OR = 1.09, 3.6 × 10(-6)) and remained significant after adjustment for rs748404 and vice versa. rs748404 is located 140 kb centromeric of the TP53BP1 gene that has been implicated in lung cancer risk. Two fully correlated, nonsynonymous coding variants in TP53BP1, rs2602141 (Q1136K) and rs560191 (E353D) showed association with lung cancer in our sample set; however, this association did not remain significant after adjustment for rs748404. Our data show that 1 or more lung cancer risk variants of genome-wide significance and distinct from the coding variants in TP53BP1 are located at 15q15.2.

Resection Rate and Outcome of Pulmonary Resections for Non–Small-Cell Lung Cancer: A Nationwide Study From Iceland

Background: The proportion of patients with non–small-cell lung cancer (NSCLC) who undergo surgery with curative intent is one measure of effectiveness in treating lung cancer. To the best of our knowledge, surgical resection rate (SRR) for a whole nation has never been reported before. We studied the SRR and surgical outcome of NSCLC patients in Iceland during a recent 15-year period. Methods: This was a retrospective study of all pulmonary resections performed with curative intent for NSCLC in Iceland from 1994 to 2008. Information was retrieved from medical records and from the Icelandic Cancer Registry. Patient demographics, postoperative tumor, node, metastasis stage, overall survival, and complication rates were compared over three 5-year periods. Results: Of 1530 confirmed cases of NSCLC, 404 were resected, giving an SRR of 26.4%, which did not change significantly during the study period. Minor and major complication rates were 37.4% and 8.7%, respectively. Operative mortality rates were 0.7% for lobectomy, 3.3% for pneumonectomy, and 0% for lesser resection. Five-year survival after all procedures was 40.7% and improved from the first to the last 5-year period (34.8% versus 43.8%, p = 0.04). Five-year survival for stages I and II together was 46.8%, with no significant change in stage distribution between periods. Five-year survival after pneumonectomy was 22.0%, which was significantly lower than for lobectomy (44.6%) and lesser resection (40.7%) (p < 0.005). Unoperated patients had a 5-year survival of 4.8%, as compared to 12.4% for all the NSCLC patients together. Conclusion: Compared with most other published studies, the SRR of NSCLC in Iceland is high. Short-term outcome is good, with a low rate of major complications and an operative mortality of only 1.0%. Five-year survival improved significantly over the study period.