Suspenseful , thrilling and well-paced underwater adventure about divers who locate a a shipwrecked treasure and morphine . This is an intense and engrossing movie with agreeable performances and good rendering of maritime action . The hit smash of ¨ Jaws ¨ by Steven Spielberg prompted this screen rendition of another Peter Benchley book . It concerns about an innocent couple ( Nick Nolte and Jacqueline Bisset ) get involved in an underwater search for treasures in the island Bermuda . They descend deep into the big blue without the aid of any kind of breathing apparatus, though sometimes use scubas . The frogmen get excited when they accidentally discover what they believe is a vast sunken treasure. They find a shipwrecked galleon and a crashed WWII vessel plenty of dope . They find a historic wreck, but nearby is a wrecked ship with a large quantity of morphine . Romer and Gail want the treasure; their diving partners also want the drugs . Dangerous criminals realize the ship and dope are submerged somewhere in the area . When the bad guys learn that the couple has located the drugs, Romer and Gail find themselves in mortal peril . Exciting and well-paced underwater adventure about a marriage that in the process they are threatened and then must thwart the enemies. The team of divers faces danger when they attempt to retrieve goods from a Spanish ship , as they spend time in shark-infested water and are helped by a treasure-seeker ( Robert Shaw ) and his underling ( Robert Tessier ) and confront nasty drug-lord ( Louis Gossett Jr ). The four divers set off on a perilous expedition in search of legendary treasure of a mysterious galleon resting in ocean floor and take back drug into the ship .The pace moves along nicely and production values are on the high scale . This is an amusing seagoing adventure in which the ocean deep figure prominently , though this time guarding sunken treasure . The action is plentiful with undersea excitement with terrifying underwater sequences. The film is spirited, lively and at times rather frightening light amusing . Made mainly as vehicle for Nick Nolte and Jacqueline Bisset , they show particularly in the technical excellence of the underwater scenes . They show off their considerable screen presence, both attractive and slender . Lightweight entertainment notable for sunny outdoors and underwater photography as well as Bisset in a bathing suit, a glamorous bikini and of course her famous wet T-shirt. Jacqueline Bisset fans will ask no more than the sight of their star in a swimsuit involved in this fast-moving sunken treasure yarn.This waterlogged story is packed with gorgeous cinematography by Christopher Challis who manage to keep this afloat with fab footage maritime as expert cameraman ; furthermore pulsating musical score by the classic John Barry . The movie was spectacularly shot in Bermuda , Australia and British Virgin Islands . The motion picture is professionally directed by Peter Yates ( Bullit ) though drags in some places and is overlong . In the 2000s was realized a special remake of this story with Paul Walker and Jessica Alba in similar roles to Nolte and Bisset titled ¨ Into the blue ¨.
Based on a novel by Peter Benchley and written by the one-hit wonder author himself, THE DEEP isn't half as interesting as it sounds. This is an exceptionally dull movie, enlivened by only a few peripheral pleasures. Watching people swim about slowly underwater is one of my pet movie hates (which is why some of the Bond films don't exactly thrill me). I mean, it's cool that actors get to act underwater, but so what? Underwater scenes are just there for padding and take up half of this film's running time. The rest is taken up with dialogue between uninvolving characters and some half-hearted attempts at suspense when Louis Gossett Jr. brings in his strong arm gang to retrieve treasure for themselves.This is a film that rightly or wrongly appears to have achieved (ahem) prominence due to Jacqueline Bisset's appearance in a wet t-shirt, which no doubt whetted the appetites of many an adolescent viewer. As well as Bisset, the film is visually superior with rich underwater photography accompanied by an effective John Barry score which helps bring out the beauty of "the deep". It's just that so little happens during the two hour length you'll wonder why they bothered.Sure, there's an involving chase between a truck and two bikes, a cool fight scene involving an outboard motor (!) and a fun climax involving a giant eel and Louis Gossett Jr's head, but that's about all the excitement you'll get out of this movie (okay, perhaps Jacqueline should go in there too). Shaw seems wasted in a repeat of his salty old sea-dog role from JAWS, with an accent that changes every couple of minutes; Nolte is fresh-faced but boring as the young hero, and Gossett Jr. doesn't get to be near nasty enough as the baddie of the piece. Eli Wallach is similarly wasted. THE DEEP - occasionally fun, but mostly turgid and padded endlessly.
Overall, Ion Reporter offered the most attractive performance among the individual callers. This study suggests combined strategies to maximize sensitivity and positive predictive value in variant calling using IONT deep sequencing.
The BAM files generated from deep sequencing and aligned by Ion Torrent Variant Server (ITV) had mean coverage depth of 1406; mean coverage of the 1 Mb target region was 95.6% at 100X (exceeding that in all but two samples) and 72.4% at 800X.
The application of next-generation sequencing in cancer has revealed the genomic landscape of many tumour types and is nowadays routinely used in research and clinical settings. Multiple algorithms have been developed to detect somatic variation from sequencing data using either paired tumour-blood or tumour-only samples. Most of these methods have been developed and evaluated for the identification of somatic variation using Illumina sequencing datasets of moderate coverage. However, a comprehensive evaluation of somatic variant detection algorithms on Ion Torrent targeted deep sequencing data has not been performed.
We have applied three somatic detection algorithms, Torrent Variant Caller, MuTect2 and VarScan2, on a large cohort of ovarian cancer patients comprising of 208 paired tumour-blood samples and 253 tumour-only samples sequenced deeply on Ion Torrent Proton platform across 330 amplicons. Subsequently, the concordance and performance of the three somatic variant callers were assessed.
Our results suggest that caution should be taken when applying state-of-the-art somatic variant algorithms to Ion Torrent targeted deep sequencing data. Better quality control procedures and strategies that combine results from multiple methods should ensure that higher accuracy is achieved. This is essential to ensure that results from bioinformatics pipelines using Ion Torrent deep sequencing can be robustly applied in cancer research and in the clinic.
However, identifying somatic variants still remains a challenge due to their low allelic fraction as well as biological and technical issues such as contamination of the sample by non-malignant cells, tumour genetic heterogeneity and template degradation due to formalin-fixed and paraffin-embedded specimens (FFPE) [7, 8]. Among the various NGS platforms, Ion Torrent Targeted (IONT) sequencing is one of the commonly used technologies for targeted deep sequencing [9,10,11]. IONT sequencing typically reaches depth of more than 1000X even with FFPE templates, which makes it an ideal platform to identify somatic variants with variable allelic fraction. Yet, like all sequencing technologies, IONT has its drawbacks. It is PCR (primer) based for library construction and measures pH changes rather than optical signals, thus introducing biases and errors different from technologies that use probe-capture for library construction and fluorescence reads . For instance, the quality of base calling accuracy generated by IONT platform is lower than other sequencing platforms, especially for INDEL events . In addition, IONT is more vulnerable to homopolymer errors compared to other platforms .
Our study reported low concordance across the methods for somatic SNVs calling, which has also been highlighted in several previous studies for other types of NGS datasets [19, 20, 36]. Among the three callers, MuTect2 identified the largest number of somatic SNVs, but they were in poor agreement with other tools. This suggests that MuTect2 is less stringent and most of the calls are likely to be false positives for IONT data. MuTect2 utilises the somatic genotyping engine of the original MuTect algorithm which was developed to have higher sensitivity for mutations with allelic fractions as low as 0.1 and below . However, it is questionable whether such sensitivity is practically needed when interrogating diagnostic and actionable variants in tumour tissues . For example, in a tissue sample with malignant cell DNA content of 50%, the rest comes from non-malignant cells. Detecting a pathogenic or actionable variant at an allelic fraction of 0.1 or even 1, does not necessarily determine whether it is present in malignant or non-malignant cells. In comparison to MuTect2, TVC returned the lowest number of SNV calls, most of which overlapped with calls from other tools. This confirmed the observation reported in a previous study which suggested the reasonable trade-off between sensitivity and specificity of TVC . One advantage of our study is that we also investigate the discrepancies in INDEL calling. MuTect2 also showed the least concordance among methods in detecting INDELs. Additionally, lower agreement among all three tools was also revealed, which indicated a greater challenge to call INDELs compared to SNVs. Another strength of our study is that we also compared the performance of callers in unpaired tumour-only samples, as most of the clinical samples submitted for NGS are tumour-only FFPE samples . We observed similar performance of MuTect2 and TVC in detecting both SNVs and INDELs in unpaired samples. For unpaired samples, the inference on whether a mutation is somatic was based on their frequency in the population. Although this was an approximation, this gave us a way to compare the two methods in their ability to call somatic variants. The discrepancies we observed among all somatic variant callers might be due to the different statistical models and assumptions of these methods. More importantly, both MuTect2 and VarScan2 were developed and optimised for Illumina NGS datasets rather than IONT deep sequencing data that exhibit much higher coverage and a different error structure. 2b1af7f3a8